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    HMGB1 high mobility group B1 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 824351, updated on 15-Feb-2024

    Summary

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    Gene symbol
    HMGB1
    Gene description
    high mobility group B1
    Primary source
    Araport:AT3G51880
    Locus tag
    AT3G51880
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    AtHMGB1; high mobility group B1; NFD1; NUCLEOSOME/CHROMATIN ASSEMBLY FACTOR D1
    Summary
    Encodes a protein belonging to the subgroup of HMGB (high mobility group B) proteins that have a distinctive DNA-binding motif, the HMG-box domain. The motif confers non-sequence specific interaction with linear DNA and structure-specific binding to distorted DNA sites. The HMGB proteins are involved in the assembly of nucleoprotein complexes. Can be phosphorylated by CK2alpha. In interphase cells, HMGB1 is found throughout the nucleus, whereas in mitotic cells it is not chromatin-associated.
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    Genomic context

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    See HMGB1 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    9
    Sequence:
    Chromosome: 3; NC_003074.8 (19246936..19249200, complement)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene cation exchanger 3 Neighboring gene Mitochondrial substrate carrier family protein Neighboring gene Clathrin light chain protein Neighboring gene sulfate transporter 3;1

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003074.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Deciphering the role of the AT-rich interaction domain and the HMG-box domain of ARID-HMG proteins of Arabidopsis thaliana. Roy A, et al. Plant Mol Biol, 2016 Oct. PMID 27503561
    2. Paraformaldehyde Fixation May Lead to Misinterpretation of the Subcellular Localization of Plant High Mobility Group Box Proteins. Li MW, et al. PLoS One, 2015. PMID 26270959, Free PMC Article
    3. Role of HMGB proteins in chromatin dynamics and telomere maintenance in Arabidopsis thaliana. Schrumpfová PP, et al. Curr Protein Pept Sci, 2011 Mar. PMID 21348847
    4. The expression level of the chromatin-associated HMGB1 protein influences growth, stress tolerance, and transcriptome in Arabidopsis. Lildballe DL, et al. J Mol Biol, 2008 Dec 5. PMID 18822296
    5. Arabidopsis chromatin-associated HMGA and HMGB use different nuclear targeting signals and display highly dynamic localization within the nucleus. Launholt D, et al. Plant Cell, 2006 Nov. PMID 17114349, Free PMC Article

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Results show not only HMGB1 was associated with interphase but also with metaphase chromosomes in Arabidopsis.
      Title: Paraformaldehyde Fixation May Lead to Misinterpretation of the Subcellular Localization of Plant High Mobility Group Box Proteins.
    2. AtHMGB1 does not affect telomerase activity and AtHMGB1 loss or overexpression does not cause any obvious changes in chromatin architecture.
      Title: Role of HMGB proteins in chromatin dynamics and telomere maintenance in Arabidopsis thaliana.
    3. The lack and overexpression of HMGB1 affect certain aspects of plant growth and stress tolerance and it has a marked impact on the transcriptome.
      Title: The expression level of the chromatin-associated HMGB1 protein influences growth, stress tolerance, and transcriptome in Arabidopsis.
    4. The subcellular localization of Arabidopsis thaliana HMGA, HMGB1, and HMGB5, reveals that they localize to the cell nucleus. They display a speckled distribution pattern throughout the chromatin of interphase nuclei.
      Title: Arabidopsis chromatin-associated HMGA and HMGB use different nuclear targeting signals and display highly dynamic localization within the nucleus.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_001084800.2
    NM_001203133.1
    NM_001339538.1
    NM_115047.3
    NM_202684.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables chromatin binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables structural constituent of chromatin TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of chromatin TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    colocalizes_with nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    high mobility group B1
    NP_001078269.1
    • high mobility group B1 (HMGB1); FUNCTIONS IN: chromatin binding, structural constituent of chromatin, DNA binding, sequence-specific DNA binding transcription factor activity; INVOLVED IN: chromatin assembly or disassembly; LOCATED IN: cytosol, chromatin, nuclear chromatin, nucleus; EXPRESSED IN: 26 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: High mobility group, superfamily (InterPro:IPR009071), High mobility group, HMG1/HMG2 (InterPro:IPR000910); BEST Arabidopsis thaliana protein match is: high mobility group B3 (TAIR:AT1G20696.3); Has 22052 Blast hits to 13496 proteins in 726 species: Archae - 26; Bacteria - 633; Metazoa - 9856; Fungi - 2535; Plants - 1397; Viruses - 386; Other Eukaryotes - 7219 (source: NCBI BLink).
    NP_001190062.1
    • high mobility group B1 (HMGB1); CONTAINS InterPro DOMAIN/s: High mobility group, superfamily (InterPro:IPR009071), High mobility group, HMG1/HMG2 (InterPro:IPR000910); BEST Arabidopsis thaliana protein match is: high mobility group B3 (TAIR:AT1G20696.3).
    NP_190756.1
    • high mobility group B1 (HMGB1); FUNCTIONS IN: chromatin binding, structural constituent of chromatin, DNA binding, sequence-specific DNA binding transcription factor activity; INVOLVED IN: chromatin assembly or disassembly; LOCATED IN: cytosol, chromatin, nuclear chromatin, nucleus; EXPRESSED IN: 26 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: High mobility group, superfamily (InterPro:IPR009071), High mobility group, HMG1/HMG2 (InterPro:IPR000910); BEST Arabidopsis thaliana protein match is: high mobility group B3 (TAIR:AT1G20696.3); Has 22052 Blast hits to 13496 proteins in 725 species: Archae - 26; Bacteria - 633; Metazoa - 9857; Fungi - 2534; Plants - 1397; Viruses - 386; Other Eukaryotes - 7219 (source: NCBI BLink).
    NP_974413.1
    • high mobility group B1 (HMGB1); FUNCTIONS IN: chromatin binding, structural constituent of chromatin, DNA binding, sequence-specific DNA binding transcription factor activity; INVOLVED IN: chromatin assembly or disassembly; LOCATED IN: cytosol, chromatin, nuclear chromatin, nucleus; EXPRESSED IN: 26 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: High mobility group, superfamily (InterPro:IPR009071), High mobility group, HMG1/HMG2 (InterPro:IPR000910); BEST Arabidopsis thaliana protein match is: high mobility group B3 (TAIR:AT1G20696.3); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_003074.8 Reference assembly

      Range
      19246936..19249200 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001084800.2 → NP_001078269.1  high mobility group B1 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001078269.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      O49595, Q3EAL6
      UniProtKB/TrEMBL
      A0A178VIW4
      Conserved Domains (1) summary
      pfam00505
      Location:53 → 121
      HMG_box; HMG (high mobility group) box

    2. NM_202684.3 → NP_974413.1  high mobility group B1 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_974413.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VHC4
      Conserved Domains (1) summary
      pfam00505
      Location:53 → 121
      HMG_box; HMG (high mobility group) box

    3. NM_001339538.1 → NP_001327501.1  high mobility group B1 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      O49595, Q3EAL6
      UniProtKB/TrEMBL
      A0A178VIW4
      Conserved Domains (1) summary
      pfam00505
      Location:53 → 121
      HMG_box; HMG (high mobility group) box

    4. NM_115047.3 → NP_190756.1  high mobility group B1 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_190756.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      O49595, Q3EAL6
      UniProtKB/TrEMBL
      A0A178VIW4
      Conserved Domains (1) summary
      pfam00505
      Location:53 → 121
      HMG_box; HMG (high mobility group) box

    5. NM_001203133.1 → NP_001190062.1  high mobility group B1 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001190062.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      F4J5M5
      Conserved Domains (1) summary
      pfam00505
      Location:53 → 121
      HMG_box; HMG (high mobility group) box
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O49595.1

    Gene LinkOut

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