PDB entry 3afa

View 3afa on RCSB PDB site
Description: The human nucleosome structure
Class: structural protein/DNA
Keywords: histone-fold, DNA-binding protein, Chromosomal protein, Citrullination, DNA-binding, Methylation, Nucleosome core, Nucleus, Phosphoprotein, Isopeptide bond, Antibiotic, Antimicrobial, STRUCTURAL PROTEIN-DNA complex
Deposited on 2010-02-24, released 2010-05-26
The last revision prior to the SCOPe 2.07 freeze date was dated 2012-07-18, with a file datestamp of 2012-07-13.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: 0.24
AEROSPACI score: 0.29 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Histone H3.1
    Species: Homo sapiens [TaxId:9606]
    Gene: H3.1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3afaa_
  • Chain 'B':
    Compound: histone h4
    Species: Homo sapiens [TaxId:9606]
    Gene: H4
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3afab_
  • Chain 'C':
    Compound: Histone H2A type 1-B/E
    Species: Homo sapiens [TaxId:9606]
    Gene: H2A
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3afac_
  • Chain 'D':
    Compound: Histone H2B type 1-J
    Species: Homo sapiens [TaxId:9606]
    Gene: H2B
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3afad_
  • Chain 'E':
    Compound: Histone H3.1
    Species: Homo sapiens [TaxId:9606]
    Gene: H3.1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3afae_
  • Chain 'F':
    Compound: histone h4
    Species: Homo sapiens [TaxId:9606]
    Gene: H4
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3afaf_
  • Chain 'G':
    Compound: Histone H2A type 1-B/E
    Species: Homo sapiens [TaxId:9606]
    Gene: H2A
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3afag_
  • Chain 'H':
    Compound: Histone H2B type 1-J
    Species: Homo sapiens [TaxId:9606]
    Gene: H2B
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3afah_
  • Chain 'I':
    Compound: 146-mer DNA
  • Chain 'J':
    Compound: 146-mer DNA
  • Heterogens: CL, MN, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3afaA (A:)
    gshmartkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqk
    stellirklpfqrlvreiaqdfktdlrfqssavmalqeaceaylvglfedtnlcaihakr
    vtimpkdiqlarrirgera
    

    Sequence, based on observed residues (ATOM records): (download)
    >3afaA (A:)
    phryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqeace
    aylvglfedtnlcaihakrvtimpkdiqlarrirger
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3afaB (B:)
    gshmsgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrg
    vlkvflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >3afaB (B:)
    niqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrktvtam
    dvvyalkrqgrtlygfgg
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3afaC (C:)
    gshmsgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavle
    yltaeilelagnaardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavll
    pkkteshhkakgk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3afaC (C:)
    rakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleyltaeilelagnaa
    rdnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpk
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3afaD (D:)
    gshmpepaksapapkkgskkavtkaqkkdgkkrkrsrkesysiyvykvlkqvhpdtgiss
    kamgimnsfvndiferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtk
    avtkytsak
    

    Sequence, based on observed residues (ATOM records): (download)
    >3afaD (D:)
    krsrkesysiyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkrsti
    tsreiqtavrlllpgelakhavsegtkavtkytsak
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3afaE (E:)
    gshmartkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqk
    stellirklpfqrlvreiaqdfktdlrfqssavmalqeaceaylvglfedtnlcaihakr
    vtimpkdiqlarrirgera
    

    Sequence, based on observed residues (ATOM records): (download)
    >3afaE (E:)
    kphryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqeac
    eaylvglfedtnlcaihakrvtimpkdiqlarrirgera
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >3afaF (F:)
    gshmsgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrg
    vlkvflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >3afaF (F:)
    rkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakr
    ktvtamdvvyalkrqgrtlygfgg
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >3afaG (G:)
    gshmsgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavle
    yltaeilelagnaardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavll
    pkkteshhkakgk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3afaG (G:)
    ktrssraglqfpvgrvhrllrkgnyservgagapvylaavleyltaeilelagnaardnk
    ktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpk
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >3afaH (H:)
    gshmpepaksapapkkgskkavtkaqkkdgkkrkrsrkesysiyvykvlkqvhpdtgiss
    kamgimnsfvndiferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtk
    avtkytsak
    

    Sequence, based on observed residues (ATOM records): (download)
    >3afaH (H:)
    rkesysiyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkrstitsr
    eiqtavrlllpgelakhavsegtkavtkytsa
    

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.