PDB entry 6jr1

View 6jr1 on RCSB PDB site
Description: Crystal structure of the human nucleosome phased with 16 selenium atoms
Class: gene regulation/DNA
Keywords: nucleosome, chromatin, histone, selenomethionine, SAD phasing, GENE REGULATION, GENE REGULATION-DNA complex
Deposited on 2019-04-02, released 2019-10-02
The last revision prior to the SCOPe 2.07 freeze date was dated 2019-10-02, with a file datestamp of 2019-09-27.
Experiment type: XRAY
Resolution: 2.4 Å
R-factor: N/A
AEROSPACI score: 0.23 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Histone H3.1
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: histone h4
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6jr1b_
  • Chain 'C':
    Compound: Histone H2A type 1-B/E
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA
    Database cross-references and differences (RAF-indexed):
    • Uniprot P04908
      • engineered mutation (68)
      • engineered mutation (88)
    Domains in SCOPe 2.07: d6jr1c_
  • Chain 'D':
    Compound: Histone H2B type 1-J
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2BJ, H2BFR
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06899
      • engineered mutation (104)
      • engineered mutation (109)
    Domains in SCOPe 2.07: d6jr1d_
  • Chain 'E':
    Compound: Histone H3.1
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: histone h4
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6jr1f_
  • Chain 'G':
    Compound: Histone H2A type 1-B/E
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA
    Database cross-references and differences (RAF-indexed):
    • Uniprot P04908
      • engineered mutation (68)
      • engineered mutation (88)
    Domains in SCOPe 2.07: d6jr1g_
  • Chain 'H':
    Compound: Histone H2B type 1-J
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2BJ, H2BFR
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06899
      • engineered mutation (104)
      • engineered mutation (109)
    Domains in SCOPe 2.07: d6jr1h_
  • Chain 'I':
    Compound: DNA (146-mer)
    Species: Homo sapiens [TaxId:9606]
  • Chain 'J':
    Compound: DNA (146-mer)
    Species: Homo sapiens [TaxId:9606]
  • Heterogens: MSE, CL, MN, HOH

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6jr1B (B:)
    gshmsgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrg
    vlkvflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >6jr1B (B:)
    dniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrktvta
    mdvvyalkrqgrtlygfg
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >6jr1C (C:)
    gshmsgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavle
    yltaeilemagnaardnkktriiprhlqmairndeelnkllgrvtiaqggvlpniqavll
    pkkteshhkakgk
    

    Sequence, based on observed residues (ATOM records): (download)
    >6jr1C (C:)
    rakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleyltaeilemagnaa
    rdnkktriiprhlqmairndeelnkllgrvtiaqggvlpniqavllpk
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >6jr1D (D:)
    gshmpepaksapapkkgskkavtkaqkkdgkkrkrsrkesysiyvykvlkqvhpdtgiss
    kamgimnsfvndiferiageasrlahynkrstitsreiqtavrlmlpgemakhavsegtk
    avtkytsak
    

    Sequence, based on observed residues (ATOM records): (download)
    >6jr1D (D:)
    srkesysiyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkrstits
    reiqtavrlmlpgemakhavsegtkavtkytsa
    

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >6jr1F (F:)
    gshmsgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrg
    vlkvflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >6jr1F (F:)
    rhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtyteha
    krktvtamdvvyalkrqgrtlygfg
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >6jr1G (G:)
    gshmsgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavle
    yltaeilemagnaardnkktriiprhlqmairndeelnkllgrvtiaqggvlpniqavll
    pkkteshhkakgk
    

    Sequence, based on observed residues (ATOM records): (download)
    >6jr1G (G:)
    aktrssraglqfpvgrvhrllrkgnyservgagapvylaavleyltaeilemagnaardn
    kktriiprhlqmairndeelnkllgrvtiaqggvlpniqavllpk
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >6jr1H (H:)
    gshmpepaksapapkkgskkavtkaqkkdgkkrkrsrkesysiyvykvlkqvhpdtgiss
    kamgimnsfvndiferiageasrlahynkrstitsreiqtavrlmlpgemakhavsegtk
    avtkytsak
    

    Sequence, based on observed residues (ATOM records): (download)
    >6jr1H (H:)
    rkesysiyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkrstitsr
    eiqtavrlmlpgemakhavsegtkavtkytsa
    

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.