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
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
Name, label and taxonomic scope
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Name
TetR/AcrR family transcriptional regulator
Label
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
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]
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.
PDB ID 2QKO: Crystal structure of transcriptional regulator RHA06399 from Rhodococcus sp. RHA1
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Partial definition is allowed, e.g., ":1-10" selects all residue IDs 1-10 in all chains.
Different selections can be unioned(with "or", default), intersected(with "and"), or negated(with "not"). For example, ":1-10 or :K" selects all residues 1-10 and all Lys residues. ":1-10 and :K" selects all Lys residues in the range of residue number 1-10. ":1-10 or not :K" selects all residues 1-10, which are not Lys residues.
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Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50.
Mutation analysis
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
Please input a Mol2 file
Mol2 File:
Please input an SDF file
SDF File:
Please input an XYZ file
XYZ File:
Please input an AlphaFold PAE file
AlphaFold PAE File:
Please input a file via URL
File type: URL in the same host:
Please append mmCIF files
Multiple mmCIF Files:
Please input an mmCIF ID
mmCIF ID:
Please input an MMDB ID
MMDB or PDB ID:
Note: The "biological unit" is the biochemically active form of a biomolecule,
which can range from a monomer (single protein molecule) to an oligomer of 100+ protein molecules.
The "asymmetric unit" is the raw 3D structure data resolved by X-ray crystallography, NMR, or Cryo-electron microscopy. The asymmetric unit is equivalent to the biological unit in approximately 60% of structure records. In the remaining 40% of the records, the asymmetric unit represents a portion of the biological unit that can be reconstructed using crystallographic symmetry, or it represents multiple copies of the biological unit.
Please input a list of PDB/AlphaFold IDs
List of PDB, MMDB, or AlphaFold UniProt structures:
or
Note: The "biological unit" is the biochemically active form of a biomolecule,
which can range from a monomer (single protein molecule) to an oligomer of 100+ protein molecules.
The "asymmetric unit" is the raw 3D structure data resolved by X-ray crystallography, NMR, or Cryo-electron microscopy. The asymmetric unit is equivalent to the biological unit in approximately 60% of structure records. In the remaining 40% of the records, the asymmetric unit represents a portion of the biological unit that can be reconstructed using crystallographic symmetry, or it represents multiple copies of the biological unit.
Align sequence to structure
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):
Sequence to structure prediction with ESMFold
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
Your note will be saved in the HTML file when you click "File > Save File > iCn3D PNG Image".
Please input a protein/gene name
Protein/Gene name:
Please input a PubChem Compound
PubChem CID/Name/InchI:
Please input a chemical SMILES
Chemical SMILES:
Please append iCn3D PNG Image files
Multiple iCn3D PNG images:
Please input a state file
State file:
Use fixed version of iCn3D
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:
Please input the selection file
Selection file:
Collection File:
You can load a collection of structures via a file. Here are some example files
Collection file:
Structures:
Export Collections
Load a preference file
Preference file:
Load a map 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
Load a selection file via a URL
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:
Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation.
The hydrogens and partial charges of proteins and nucleotides are added using DelPhiPKa with the Amber charge and size files. The hydrogens of ligands are added using Open Babel. The partial charges of ligands are calculated using Antechamber with the Gasteiger charge method. All partial charges are calculated at pH 7.
Lipids are treated as ligands. Please use "HETATM" instead of "ATOM " for each lipid atom in your PDB file. Each phosphate in lipids is assigned with a charge of -1. You can download PQR and modify it, or prepare your PQR file using other tools. Then load the PQR file at the menu "Analysis > Load PQR/Potential".
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.
The hydrogens and partial charges of proteins and nucleotides are added using DelPhiPKa with the Amber charge and size files. The hydrogens of ligands are added using Open Babel. The partial charges of ligands are calculated using Antechamber with the Gasteiger charge method. All partial charges are calculated at pH 7.
Lipids are treated as ligands. Please use "HETATM" instead of "ATOM " for each lipid atom in your PDB file. Each phosphate in lipids is assigned with a charge of -1. You can download PQR and modify it, or prepare your PQR file using other tools. Then load the PQR file at the menu "Analysis > Load PQR/Potential".
Note: Always load a PDB file before loading a PQR or DelPhi potential file.
The PDB file can be loaded in the URL with "pdbid=" or at "File > Open File". The PQR file can be prepared at the menu "Analysis > Download PQR" with your modification or using other tools. The DelPhi potential file can be calculated at DelPhi Web Server and be exported as a Cube file.
Surface with max potential at: kT/e(25.6mV at 298K)
Note: Always load a PDB file before loading a PQR or DelPhi potential file.
The PDB file can be loaded in the URL with "pdbid=" or at "File > Open File". The PQR file can be prepared at the menu "Analysis > Download PQR" with your modification or using other tools. The DelPhi potential file can be calculated at DelPhi Web Server and be exported as a Cube file.
Note: Always load a PDB file before loading a PQR or DelPhi potential file.
The PDB file can be loaded in the URL with "pdbid=" or at "File > Open File". The PQR file can be prepared at the menu "Analysis > Download PQR" with your modification or using other tools. The DelPhi potential file can be calculated at DelPhi Web Server and be exported as a Cube file. The PQR or potential file can be accessed in a URL if it is located in the same host as iCn3D.
Surface with max potential at: kT/e(25.6mV at 298K)
Note: Always load a PDB file before loading a PQR or DelPhi potential file.
The PDB file can be loaded in the URL with "pdbid=" or at "File > Open File". The PQR file can be prepared at the menu "Analysis > Download PQR" with your modification or using other tools. The DelPhi potential file can be calculated at DelPhi Web Server and be exported as a Cube file. The PQR or potential file can be accessed in a URL if it is located in the same host as iCn3D.
Symmetry
Symmetry:
Dynamically symmetry calculation using SymD
Contact Map
Distance: Contact Type:
Interaction Analysis
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
Realign by sequence
1. Select sets below or use your current selection:
2.
Realign by structure
1. Select sets below or use your current selection.
2.
Realign two structure complexes
1. Select sets below or use your current selection:
2. Overall maximum RMSD: Å
3.
Set color spectrum across sets
1. Select sets below:
2.
Set color spectrum for residues in sets
1. Select sets below:
2.
Set color rainbow across sets
1. Select sets below:
2.
Set color rainbow for residues in sets
1. Select sets below:
2.
All interactions
Sorted interactions
2D Interaction Network
Hold Ctrl key to select multiple nodes/lines.
Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts
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)
Note: The full protein sequences with gaps in MSA are listed one by one. The sequence of the structure is listed at the top. Each sequence has a title line starting with ">".
Precalculated Multiple Sequence Alignment (MSA):
Position of the first residue in Sequences & Annotations window:
Color Sequence by:
Note: Show exons for all isoforms of the protein in the same gene as specified below.
Position of the first residue in Sequences & Annotations window:
BED file:
Track Title:
Track Text (e.g., "2 G, 5-6 RR" defines a character "G" at the position 2 and two continuous characters "RR" at positions from 5 to 6. The starting position is 1):
Track Title:
Save Selection
Name:
Share Link
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.
Select on 1D sequences: drag to select, drag again to deselect, multiple selection is allowed without Ctrl key, click "Save Selection" to save the current selection.
Select on 2D interaction diagram: click on the nodes or lines. The nodes are chains and can be united with the Ctrl key. The lines are interactions and can NOT be united. Each click on the lines selects half of the lines, i.e., select the interacting residues in one of the two chains.
Select on 3D structures: hold "Alt" and use mouse to pick, click the second time to deselect, hold "Ctrl" to union selection, hold "Shift" to select a range, press the up/down arrow to switch among atom/residue/strand/chain/structure, click "Save Selection" to save the current selection.
Save the current selection(either on 3D structure, 2D interactions, or 1D sequence): open the menu "Select -> Save Selection", specify the name and description for the selection, and click "Save".
Residue labeling: standard residue with coordinates: UPPER case letter; nonstandard residue with coordinates: the first UPPER case letter plus a period except that water residue uses the letter 'O'; residue missing coordinates: lower case letter.
Interactions
Zoom: mouse wheel; Move: left button; Select Multiple Nodes: Ctrl Key and drag an Area
Click "View > H-Bonds & Interactions" to adjust parameters and relaunch the graph
Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: contacts; Orange: disulfide bonds
Solvent Accessible Surface Area(SASA) calculated using the EDTSurf algorithm: (0-20% out is considered "in". 50-100% out is considered "out".)
Toal: Å2
Color by surface area
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): %
RMSD
Buried surface area
Select residues basen on solvent accessilbe surface area
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 residues basen on B-factor/pLDDT
Select residue based on B-factor/pLDDT. The values are in the range of 0-100.
Min B-factor/pLDDT: % Max B-factor/pLDDT: %
Legend
Distance Table
Angle Table
Translate the X,Y,Z coordinates of the structure
X: Y: Z:
Measure the angle between two vectors
Vector 1, X: Y: Z: Vector 2, X: Y: Z:
The angle is: degree.
Apply matrix to the X,Y,Z coordinates of the structure