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TetR/AcrR family transcriptional regulator

TetR/AcrR family transcriptional regulator controls genes involved in a variety of processes including antibiotic production, osmotic stress response, efflux pump expression, and multidrug resistance

Arch. IDVersionDate PublishedReview Level
1330686112018-12-13
curated
Arch. ID13306861
Version1
Date Published2018-12-13
Review Level
curated
PRK14996: TetR family transcriptional regulatorPRK14996AcrR: DNA-binding protein, AcrR family, includes nucleoid occlusion protein SlmA [Transcription]AcrR
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Sequences with this architecture
Name, label and taxonomic scope
Taxonomic scopeNameLabel
All organismsTetR/AcrR family transcriptional regulatorTetR/AcrR family transcriptional regulator controls genes involved in a variety of processes including antibiotic production, osmotic stress response, efflux pump expression, and multidrug resistance
Name, label and taxonomic scope
Tax. ExpAll organisms
NameTetR/AcrR family transcriptional regulator
LabelTetR/AcrR family transcriptional regulator controls genes involved in a variety of processes including antibiotic production, osmotic stress response, efflux pump expression, and multidrug resistance
Supporting evidence
Comments
  • members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 10450557: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 10357187: from 10450557: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 10357187: from 10450557: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 10419999: Members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain.
  • from 10419999: The founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance.
  • from 10450557: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain; some members of this architecture may contain only the HTH (TetR_N) domain
  • from 10450557: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 10451475: from 10451993: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 10451475: from 10451993: The founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump
  • from 10451547: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 10451547: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 10451983: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 10451983: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 10452004: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 10452004: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 10452006: Members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain.
  • from 10452006: The founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance.
  • from 11003849: Members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain.
  • from 11003849: The founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance.
  • from 11442015: from 10451983: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11442015: from 10451983: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11442181: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11442181: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11442206: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11442206: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11442213: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11442213: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11442215: from 10450557: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11442215: from 10450557: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11442241: from 10450557: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11442241: from 10450557: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11442245: Members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain.
  • from 11442245: The founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance.
  • from 11442247: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11442247: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11442252: from 10450557: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11442252: from 10450557: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11442256: from 10450557: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11442256: from 10450557: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11442297: from 10450557: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11442297: from 10450557: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11807513: from 10450557: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11807513: from 10450557: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11808854: from 10450557: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11808854: from 10450557: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11818308: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11818308: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11818319: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11818319: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11870575: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11870575: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11870581: from 10450557: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11870581: from 10450557: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11877024: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11877024: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11877079: Members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain.
  • from 11877079: The founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance.
  • from 11923260: from 10450557: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11923260: from 10450557: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11923264: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11923264: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11923301: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11923301: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11923315: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11923315: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11923321: from 10450557: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11923321: from 10450557: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11923331: The founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance.
  • from 11923331: Members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain.
  • from 11923355: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11923355: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11923377: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11923377: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11923388: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11923388: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11928530: from 10450557: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11928530: from 10450557: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11995497: from 10450557: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11995497: from 10450557: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11995549: from 10450557: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11995549: from 10450557: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11995559: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11995559: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11995569: from 10450557: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11995569: from 10450557: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11995583: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11995583: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11995596: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11995596: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11995605: Members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain.
  • from 11995605: The founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance.
  • from 11995677: from 10450557: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11995677: from 10450557: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11995686: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11995686: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11995699: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11995699: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
  • from 11995706: Members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain.
  • from 11995706: The founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance.
  • from 11995718: from 10450557: members of the TetR family transcriptional regulators have a conserved helix-turn-helix DNA-binding domain and a C-terminal ligand regulatory domain
  • from 11995718: from 10450557: the founding member of TetR was identified in Escherichia coli and controls the expression of the gene encoding a tetracycline efflux pump responsible for drug resistance
Protein Accession
  • OBB99380: TetR family transcriptional regulator [Mycobacterium sp. 852002-40037_SCH5390672]
  • KJB92564: TetR family transcriptional regulator [Skermanella aerolata KACC 11604]
  • P96856: RecName: Full=HTH-type transcriptional repressor KstR
  • Q8FTA6: RecName: Full=HTH-type transcriptional repressor AcnR
  • ANC72045: TetR family transcriptional regulator [Deinococcus radiodurans R1]
  • AIY14628: TetR family transcriptional regulator [Cellulophaga baltica NN016038]
  • ADB33209: transcriptional regulator, TetR family [Kribbella flavida DSM 17836]
  • AGP88391: TetR family transcriptional regulator [Alteromonas macleodii str. 'Ionian Sea U7']
  • ESZ66946: TetR family transcriptional regulator [Mesorhizobium sp. L103C120A0]
  • SEB20010: transcriptional regulator, TetR family [Paenibacillus sp. 276b]
  • SFM72380: transcriptional regulator, TetR family [Streptomyces sp. cf124]
  • KJZ66487: TetR family transcriptional regulator [Pseudomonas fluorescens]
  • P96676: RecName: Full=Uncharacterized HTH-type transcriptional regulator YdeS
  • KQL33640: TetR family transcriptional regulator [Psychrobacillus sp. FJAT-21963]
  • BAM23712: TetR/AcrR family transcriptional regulator [Streptococcus intermedius JTH08]
  • AAG31690: Pip [Streptomyces coelicolor]
  • AJS09399: TetR-family transcription regulator [Streptomyces sp. HKI 118]
  • ENO15420: TetR family transcriptional regulator [Marinobacter nanhaiticus D15-8W]
  • EDT45648: transcriptional regulator, TetR family [Bifidobacterium dentium ATCC 27678]
  • CAD47972: transcriptional repressor of the 6-hydroxy-D-nicotine oxidase gene (plasmid) [Paenarthrobacter nicotinovorans]
  • ABA41004: HnoR [Inducible expression vector pART3]
  • EEB77041: transcriptional regulator, TetR family [marine gamma proteobacterium HTCC2148]
  • EJO87875: TetR family transcriptional regulator [Mycobacterium colombiense CECT 3035]
  • KRE32111: AsnC family transcriptional regulator [Mycobacterium sp. Soil538]
  • ANL62363: TetR family transcriptional regulator protein (plasmid) [Rhizobium phaseoli]
  • KPI19077: transcriptional regulator, TetR family [Actinobacteria bacterium OK074]
  • Q6NH62: RecName: Full=HTH-type transcriptional repressor AcnR
  • Q9ZN78: RecName: Full=A-factor receptor protein; AltName: Full=A-factor-binding protein
  • P9WMD5: RecName: Full=Uncharacterized HTH-type transcriptional regulator Rv1255c
  • KPI24822: transcriptional regulator, TetR family [Actinobacteria bacterium OV320]
  • OCB57583: TetR family transcriptional regulator [Mycobacterium vulneris]
  • AAT45302: TetR-type regulator [Streptomyces tubercidicus]
  • KIF68563: TetR family transcriptional regulator [Streptomyces sp. AcH 505]
  • KZO59154: TetR family transcriptional regulator [Dietzia maris]
  • EQD87228: TetR family transcriptional regulator [Saccharopolyspora erythraea D]
  • P9WMB9: RecName: Full=HTH-type transcriptional repressor KstR2
  • P9WMC3: RecName: Full=HTH-type transcriptional repressor Rv3405c
  • KJK56262: TetR family transcriptional regulator [Saccharothrix sp. ST-888]
  • ESQ01163: TetR family transcriptional regulator [Streptomyces sp. GBA 94-10]
  • P0ACT6: RecName: Full=HTH-type transcriptional regulator UidR; AltName: Full=Gus operon repressor; AltName: Full=Uid operon repressor
  • Q8G2M8: RecName: Full=HTH-type transcriptional repressor BepR
  • KRA18580: TetR family transcriptional regulator [Acidovorax sp. Root568]
  • Q0S868: RecName: Full=HTH-type transcriptional repressor KstR
  • KZN94801: TetR family transcriptional regulator [Aeribacillus pallidus]
  • SDL45362: regulatory protein, tetR family [Microbacterium sp. cl140]
  • BAC55323: putative members of the TetR/AcrR family protein [Pseudomonas stutzeri]
  • AKU26466: TetR family transcriptional regulator [Geobacillus sp. LC300]
  • ACS83759: TetR transcriptional regulator [Nonomuraea sp. WU8817]
  • ALI23941: Transcriptional regulator, TetR family [Mycobacterium fortuitum]
  • AGN74903: TetR-type regulator [Streptomyces griseoviridis]
  • OAA98096: TetR family transcriptional regulator [Streptomyces sp. FXJ1.172]
  • OCH81749: TetR family transcriptional regulator [Gordonia sp. UCD-TK1]
  • KOG33759: TetR family transcriptional regulator [Streptomyces viridochromogenes]
  • C5A0R2: RecName: Full=HTH-type transcriptional repressor FabR
  • A6TFN2: RecName: Full=Nucleoid occlusion factor SlmA
CDD
  • COG3226: YbjK : DNA-binding transcriptional regulator YbjK [Transcription]
  • pfam13305: WHG : WHG domain
  • pfam14278: TetR_C_8 : Transcriptional regulator C-terminal region
  • PRK11552: putative DNA-binding transcriptional regulator; Provisional
  • TIGR03384: betaine_BetI : transcriptional repressor BetI
  • PRK10668: DNA-binding transcriptional repressor AcrR; Provisional
  • TIGR03613: RutR : pyrimidine utilization regulatory protein R
  • pfam08359: TetR_C_4 : YsiA-like protein, C-terminal region
  • pfam14246: TetR_C_7 : AefR-like transcriptional repressor, C-terminal region
  • PRK14996: TetR family transcriptional regulator; Provisional
  • pfam02909: TetR_C : Tetracyclin repressor, C-terminal all-alpha domain
  • pfam16859: TetR_C_11 : Bacterial transcriptional repressor C-terminal
  • TIGR03968: mycofact_TetR : mycofactocin system transcriptional regulator
  • PRK09975: DNA-binding transcriptional regulator EnvR; Provisional
  • COG1309: AcrR : DNA-binding transcriptional regulator, AcrR family [Transcription]
  • pfam00440: TetR_N : Bacterial regulatory proteins, tetR family
Gene IDs
Publications
  • PMID 12003942: Characterization of interactions between the transcriptional repressor PhlF and its binding site at the phlA promoter in Pseudomonas fluorescens F113.
  • PMID 11050092: A transcriptional regulator of a pristinamycin resistance gene in Streptomyces coelicolor.
  • PMID 25537663: Insights into the pamamycin biosynthesis.
  • PMID 14534317: Characterization of HdnoR, the transcriptional repressor of the 6-hydroxy-D-nicotine oxidase gene of Arthrobacter nicotinovorans pAO1, and its DNA-binding activity in response to L- and D-nicotine Derivatives.
  • PMID 9813285: Site-directed mutagenesis of the A-factor receptor protein: Val-41 important for DNA-binding and Trp-119 important for ligand-binding.
  • PMID 7592371: Cloning and characterization of the A-factor receptor gene from Streptomyces griseus.
  • PMID 23831227: SCO4008, a putative TetR transcriptional repressor from Streptomyces coelicolor A3(2), regulates transcription of sco4007 by multidrug recognition.
  • PMID 9643542: Involvement of two A-factor receptor homologues in Streptomyces coelicolor A3(2) in the regulation of secondary metabolism and morphogenesis.
  • PMID 2502536: Detection and properties of A-factor-binding protein from Streptomyces griseus.
  • PMID 10540289: The A-factor regulatory cascade leading to streptomycin biosynthesis in Streptomyces griseus : identification of a target gene of the A-factor receptor.
  • PMID 14757054: Crystal structure of a gamma-butyrolactone autoregulator receptor protein in Streptomyces coelicolor A3(2).
  • PMID 25092919: Structural and functional basis of transcriptional regulation by TetR family protein CprB from S. coelicolor A3(2).
  • PMID 25406313: Structural and functional characterization of a ketosteroid transcriptional regulator of Mycobacterium tuberculosis.
  • PMID 20167624: Cholesterol utilization in mycobacteria is controlled by two TetR-type transcriptional regulators: kstR and kstR2.
  • PMID 20435893: Domain cross-talk during effector binding to the multidrug binding TTGR regulator.
  • PMID 17264217: A gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into Mycobacterium tuberculosis survival in macrophages.
  • PMID 21835774: The crystal structure of the TetR family transcriptional repressor SimR bound to DNA and the role of a flexible N-terminal extension in minor groove binding.
  • PMID 21354180: Structures of the TetR-like simocyclinone efflux pump repressor, SimR, and the mechanism of ligand-mediated derepression.
  • PMID 17444523: Crystal structure of TM1030 from Thermotoga maritima at 2.3 A resolution reveals molecular details of its transcription repressor function.
  • PMID 24006471: The TetR family of regulators.
  • PMID 15944459: The TetR family of transcriptional repressors.
3-D Structures
  • 2QKOCrystal Structure Of Transcriptional Regulator Rha06399 From Rhodococcus Sp. Rha1
  • 2QWTCrystal Structure Of The Tetr Transcription Regulatory Protein From Mycobacterium Vanbaalenii
  • 2PBXVibrio Cholerae Hapr
  • 2ZB9Crystal Structure Of Tetr Family Transcription Regulator Sco0332
  • 3BJBCrystal Structure Of A Tetr Transcriptional Regulator From Rhodococcus Sp. Rha1
  • 2HXOStructure Of The Transcriptional Regulator Sco7222, A Tetr From Streptomyces Coelicolor
  • 2D6YCrystal Structure Of Transcriptional Factor Sco4008 From Streptomyces Coelicolor A3(2)
  • 1UI5Crystal Structure Of Gamma-Butyrolactone Receptor (Arpa Like Protein)
  • 4PXIElucidation Of The Structural And Functional Mechanism Of Action Of The Tetr Family Protein, Cprb From S. Coelicolor A3(2)
  • 2FBQThe Crystal Structure Of Transcriptional Regulator Pa3006
  • 4W97Structure Of Ketosteroid Transcriptional Regulator Kstr2 Of Mycobacterium Tuberculosis
  • 4ME9Crystal Structure Of A Transcriptional Regulator, Tetr Family (bce_2991) From Bacillus Cereus Atcc 10987 At 2.50 A Resolution
  • 2XDNTranscription Factor Ttgr H67a Mutant
  • 2Y2ZLigand-Free Form Of Tetr-Like Repressor Simr
  • 3DCFCrystal Structure Of Transcriptional Regulator Of The TetrACRR FAMILY (YP_290855.1) FROM THERMOBIFIDA FUSCA YX- Er1 At 2.50 A Resolution
  • 3EGQCrystal Structure Of A Tetr-Family Transcriptional Regulator (Af_1817) From Archaeoglobus Fulgidus At 2.55 A Resolution

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{"ALA":"#C8C8C8", "ARG":"#145AFF", ..., "G":"#008000", "A":"#6080FF", ...}

Residue Color File:
The custom file for the structure has two columns separated by space or tab: residue number, and score in the range of 0-100. If you click "Apply Custom Color" button, the scores 0, 50 and 100 correspond to the three colors specified below. If you click "Apply Custom Tube", the selected residues will be displayed in a style similar to "B-factor Tube".

Custom File:

1.
Score to Color: 0: 50: 100:
or

2.
You can define your own reference numbers in a custom file using Excel, and then export it as a CSV file. An example file is shown below with cells separated by commas.
refnum,11,12,,21,22,,10C,11C,20C
1TUP_A,100,101,,,132,,,,
1TUP_B,110,111,,141,142,,,,
1TUP_C,,,,,,,200,201,230
The first row defines the reference residue numbers, which could be any strings. The 1st cell could be anything. The rest cells are reference residue numbers (e.g., 11, 21, 10C, etc.) or empty cells. Each chain has a separate row. The first cell of the second row is the chain ID "1TUP_A". The rest cells are the corresponding real residue numbers for reference residue numbers in the first row. For example, the reference numbers for residues 100, 101, and 132 in the chain 1TUP_A are 11, 12, and 22, respectively. The fourth row shows another set of reference numners for the chain "1TUP_C". It could be a chain from a different structure.

To select all residues corresponding to the reference numbers, you can simplay replace ":" with "%" in the Specification. For example, "%12" selects the residue 101 in 1TUP_A and the residue 111 in 1TUP_B. ".A%12" has the chain "A" filter and selects the residue 101 in 1TUP_A.

Custom File:

Enter the PDB IDs or MMDB IDs of the structures:

ID1:       ID2:

VAST+ based on VAST:    

VAST+ based on TM-align:

Enter two AlphaFold Uniprot IDs:

ID1:       ID2:

All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).

Chain IDs:



(Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".)

All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).

Chain IDs:

The sequence alignment (followed by structure alignment) is based on residue numbers in the First/Master chain:



(Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".)

All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).

Chain IDs:

Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50.


Option 1:

Option 2:
All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).

Chain IDs:

Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50.


Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[uppercase PDB ID or AlphaFold UniProt ID]_[Chain Name]_[Residue Number]_[One Letter Mutant Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A".
If you load a custom structure without PDB or UniProt ID, you can open "Seq. & Annotations" window and find the chain ID such as "stru_A". The part before the underscore is the structure ID, which can be used to specify the mutation such as "stru_A_...". Remember to choose "Show Mutation in: Current Page".

Mutations:


ID Type: PDB IDAlphaFold UniProt ID

Show Mutation in: Current PageNew Page



Mol2 File:
SDF File:
XYZ File:
AlphaFold PAE File:

File type:
URL in the same host:
Multiple mmCIF Files:
mmCIF ID:
MMDB or PDB ID:




Note: The "biological unit" is the biochemically active form of a biomolecule,
List of PDB, MMDB, or AlphaFold UniProt structures:



or


Note: The "biological unit" is the biochemically active form of a biomolecule,
Enter a protein sequence ID (or FASTA sequence) and the aligned protein accession, which can be found using the BLAST search with the protein sequence ID or FASTA sequence as input. If the protein accession is not a PDB chain, the corresponding AlphaFold UniProt structure is used.

Protein Sequence ID(NCBI protein accession of a sequence):
or FASTA sequence:


Aligned Protein Accession (or a chain of a PDB):
The sequence to structure prediction is done via ESM Metagenomic Atlas. The sequence should be less than 400 characters. For any sequence longer than 400, please see the discussion here.

FASTA sequence:


Your note will be saved in the HTML file when you click "File > Save File > iCn3D PNG Image".


Protein/Gene name:
PubChem CID/Name/InchI:
Chemical SMILES:
Multiple iCn3D PNG images:
State file:
Since January 6, 2021, you can show the original view with the archived version of iCn3D by pasting your URL below and click "Show Originial View". Note the version in the parameter "v" was used to replace "full.html" with "full_[v].html" in the URL.

Share Link URL:


Selection file:
Collection File:

You can load a collection of structures via a file. Here are some example files

Collection file:

Structures:





Preference file:
Note: Always load a PDB file before loading map files. If you don't specify the threshold below, a default one will be chosen.


2fofc contour at default threshold or at: σ




fofc contour at default threshold or at: σ





Note: Always load a PDB file before loading map files. If you don't specify the threshold below, a default one will be chosen.


2fofc contour at default threshold or at: σ
URL in the same host:



fofc contour at default threshold or at: σ
URL in the same host:




Click in the input box to use the color picker:

Custom Color:
Grid Size: Salt Concentration: M

Potential contour at: kT/e(25.6mV at 298K)



Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation.

Grid Size: Salt Concentration: M

Surface with max potential at: kT/e(25.6mV at 298K)

Surface: Opacity: Wireframe:



Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation.

Potential contour at: kT/e(25.6mV at 298K)

Grid Size: Salt Concentration: M

PQR File:

Phi File:

Cube File:


Note: Always load a PDB file before loading a PQR or DelPhi potential file.

Surface with max potential at: kT/e(25.6mV at 298K)

Surface: Opacity: Wireframe:

Grid Size: Salt Concentration: M

PQR File:

Phi File:

Cube File:


Note: Always load a PDB file before loading a PQR or DelPhi potential file.

Potential contour at: kT/e(25.6mV at 298K)

Grid Size: Salt Concentration: M

PQR URL in the same host:

Phi URL in the same host:

Cube URL in the same host:


Note: Always load a PDB file before loading a PQR or DelPhi potential file.

Surface with max potential at: kT/e(25.6mV at 298K)

Surface: Opacity: Wireframe:

Grid Size: Salt Concentration: M

PQR URL in the same host:

Phi URL in the same host:

Cube URL in the same host:


Note: Always load a PDB file before loading a PQR or DelPhi potential file.


Symmetry:       

Distance: Contact Type:


1. Choose interaction types and their thresholds:
Hydrogen Bonds    
Å   
Salt Bridge/Ionic    
Å   
Contacts/Interactions    
Å   
Halogen Bonds    
Å   
π-Cation    
Å   
π-Stacking    
Å   
2. Select the first set:
3. Select the second set:
4.

Sort Interactions on:

to show two lines of residue nodes

to show map

with atom details

to show interactions with strength parameters in 0-200:
Helix or Sheet: Coil or Nucleotide: Disulfide Bonds:
Hydrogen Bonds: Salt Bridge/Ionic: Contacts:
Halogen Bonds: π-Cation: π-Stacking:
(Note: you can also adjust thresholds at #1 to add/remove interactions.)


5. and select new sets
1. Select sets below
or use your current selection:


2.

1. Select sets below or use your current selection.


2.

1. Select sets below or use your current selection:


2. Overall maximum RMSD: Å

3.

1. Select sets below:

2.

1. Select sets below:

2.

1. Select sets below:

2.

1. Select sets below:

2.

  Hold Ctrl key to select multiple nodes/lines.
Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts
Magenta: Halogen Bonds; Red: π-Cation; Blue: π-Stacking

        Scale:

Hold Ctrl key to select multiple nodes.   
        Scale:

Note: Nodes/Residues can be dragged. Both nodes and dashed lines/interactions can be clicked to select residues.    
Color legend for interactions (dashed lines):
Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts
Magenta: Halogen Bonds; Red: π-Cation; Blue: π-Stacking

    Scale:

Hold Ctrl key to select multiple nodes.   
        Scale:

Hold Ctrl key to select multiple nodes.   
        Scale:

051015202530
Expected position error (Angstroms)

Contour at: σ
Contour at: σ
Contour at: % of maximum EM values
1. Select the first set:

2. Sphere with a radius: Å

3. Select the second set to apply the sphere:

4. the sphere around the first set of atoms

interacting/contacting residue pairs in a file
Note: The membranes are parallel to the X-Y plane. The center of the membranes is at Z = 0.

1. Extracellular membrane Z-axis position: Å

2. intracellular membrane Z-axis position: Å

3. the adjusted membranes

Note: The membranes are parallel to the X-Y plane. The center of the membranes is at Z = 0.

1. Z-axis position of the first X-Y plane: Å

2. Z-axis position of the second X-Y plane: Å

3. the region between the planes to Defined Sets

1. Text:
2. Size:
3. Color:
4. Pick TWO atoms while holding "Alt" key
5.
1. Text:
2. Size:
3. Color:
4.
Color for all labels:

1. Pick TWO atoms while holding "Alt" key
2. Line Color:
3.
1. Pick TWO atoms while holding "Alt" key
2. Color:
3.
1. Select two sets
First set:
Second set:
2. Color:

3.
1. Select two sets
First set:
Second set:
2. Line style:

3. Line radius:

4. Color:

5. Opacity:

6.    
1. Select a set:

2. Shape:

3. Radius:

4. Color:

5. Opacity:

6.    
1. Select sets for pairwise distances
First sets:
Second sets:
2.
Note: Each set is represented by a vector, which is the X-axis of the principle axes. The angles between the vectors are then calculated.

1. Select sets for pairwise angles
First sets:
Second sets:
2.
1. Pick TWO atoms while holding "Alt" key
2.
Line Radius:    (for stabilizers, hydrogen bonds, distance lines, default 0.1)
Coil Radius:    (for coils, default 0.3)
Stick Radius:    (for sticks, default 0.4)
Cross-Linkage Radius:    (for cross-linkages, default 0.4)
Trace Radius:    (for C alpha trace, O3' trace, default 0.4)
Ribbon Thickness:    (for helix and sheet ribbons, nucleotide ribbons, default 0.2)
Protein Ribbon Width:    (for helix and sheet ribbons, default 1.3)
Nucleotide Ribbon Width:    (for nucleotide ribbons, default 0.8)
Ball Scale:    (for styles 'Ball and Stick' and 'Dot', default 0.3)
   
Note: The following parameters will be saved in cache. You just need to set them once.

1. Shininess:    (for the shininess of the 3D objects, default 40)

2. Three directional lights:
Key Light:    (for the light strength of the key light, default 0.8)
Fill Light:    (for the light strength of the fill light, default 0.4)
Back Light:    (for the light strength of the back light, default 0.2)

3. Thickness:
Line Radius:    (for stabilizers, hydrogen bonds, distance lines, default 0.1)
Coil Radius:    (for coils, default 0.3)
Stick Radius:    (for sticks, default 0.4)
Cross-Linkage Radius:    (for cross-linkages, default 0.4)
Trace Radius:    (for C alpha trace, O3' trace, default 0.4)
Ribbon Thickness:    (for helix and sheet ribbons, nucleotide ribbons, default 0.2)
Protein Ribbon Width:    (for helix and sheet ribbons, default 1.3)
Nucleotide Ribbon Width:    (for nucleotide ribbons, default 0.8)
Ball Scale:    (for styles 'Ball and Stick' and 'Dot', default 0.3)

4. Show Glycan Cartoon:    (0: hide, 1: show, default 0)

5. Show Membrane:    (0: hide, 1: show, default 1)

6. Enlarge Command Window:    (0: Regular, 1: Large, default 0)

   
Note: The following parameters will be saved in cache. You just need to set them once.





Note: Show exons for all isoforms of the protein in the same gene as specified below.

NCBI Gene ID:    

Position of the first residue in Sequences & Annotations window:

Name:



1. URLs Used in Browsers

Please copy one of the URLs below. They show the same result.
(To add a title to share link, click "Windows > Your Note" and click "File > Share Link" again.)

Original URL with commands:


Lifelong Short URL:(To replace this URL, send a pull request to update share.html at iCn3D GitHub)


Lifelong Short URL + Window Title:(To update the window title, click "Analysis > Your Note/Window Title".)


2. Commands Used in Jupyter Noteboook

Please copy the following commands into a cell in Jupyter Notebook to show the same result.
More details are at https://github.com/ncbi/icn3d/tree/master/jupyternotebook.



Annotations: 
All  Conserved Domains  ClinVar  Functional Sites  
Custom  3D Domains  SNPs  PTM (UniProt)  
Disulfide Bonds  Interactions  Cross-Linkages  Transmembrane  
Ig Domains  




Zoom: mouse wheel;     Move: left button;     Select Multiple Nodes: Ctrl Key and drag an Area   
       
Force on Nodes:
   Label Size:    
Internal Edges:
Solvent Accessible Surface Area(SASA) calculated using the EDTSurf algorithm:
(0-20% out is considered "in". 50-100% out is considered "out".)

Toal: 2

Color each residue based on the percentage of solvent accessilbe surface area. The color ranges from blue, to white, to red for a percentage of 0, 35(variable), and 100, respectively.

Middle Percentage(White): %



Select residue based on the percentage of solvent accessilbe surface area. The values are in the range of 0-100.

Min Percentage: %
Max Percentage: %


Select residue based on B-factor/pLDDT. The values are in the range of 0-100.

Min B-factor/pLDDT: %
Max B-factor/pLDDT: %


X: Y: Z:
Vector 1, X: Y: Z:
Vector 2, X: Y: Z:



The angle is: degree.

0: 4: 8: 12:
1: 5: 9: 13:
2: 6: 10: 14:
3: 7: 11: 15:
Choose an Ig template for selected residues:



Choose an Ig template to align with selected residues:



Conserved domains in this architecture
AccessionShort nameTitle
COG1309AcrRDNA-binding protein, AcrR family, includes nucleoid occlusion protein SlmA [Transcription]
cl33054PRK14996TetR family transcriptional regulator

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