PDB entry 5jrg

View 5jrg on RCSB PDB site
Description: Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF)
Class: DNA binding protein/DNA
Keywords: histone fold, DNA binding, nucleus, chromatin formation, nucleosome, AP-site, DNA BINDING PROTEIN-DNA complex
Deposited on 2016-05-06, released 2017-03-08
The last revision prior to the SCOPe 2.07 freeze date was dated 2017-10-04, with a file datestamp of 2017-09-29.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: N/A
AEROSPACI score: 0.21 (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): Domains in SCOPe 2.07: d5jrga_
  • 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: d5jrgb_
  • 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): Domains in SCOPe 2.07: d5jrgc_
  • Chain 'D':
    Compound: Histone H2B type 1-J
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2BJ, H2BFR
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5jrgd_
  • 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): Domains in SCOPe 2.07: d5jrge_
  • 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: d5jrgf_
  • 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): Domains in SCOPe 2.07: d5jrgg_
  • Chain 'H':
    Compound: Histone H2B type 1-J
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2BJ, H2BFR
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5jrgh_
  • Chain 'I':
    Compound: DNA (145-mer)
    Species: Homo sapiens [TaxId:9606]
  • Chain 'J':
    Compound: DNA (145-mer)
    Species: Homo sapiens [TaxId:9606]
  • Heterogens: CL, MN, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5jrgA (A:)
    gshmartkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqk
    stellirklpfqrlvreiaqdfktdlrfqssavmalqeaceaylvglfedtnlcaihakr
    vtimpkdiqlarrirgera
    

    Sequence, based on observed residues (ATOM records): (download)
    >5jrgA (A:)
    phryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqeace
    aylvglfedtnlcaihakrvtimpkdiqlarrirger
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5jrgB (B:)
    gshmsgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrg
    vlkvflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >5jrgB (B:)
    niqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrktvtam
    dvvyalkrqgrtlygfgg
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5jrgC (C:)
    gshmsgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavle
    yltaeilelagnaardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavll
    pkkteshhkakgk
    

    Sequence, based on observed residues (ATOM records): (download)
    >5jrgC (C:)
    akaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleyltaeilelagnaar
    dnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpk
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5jrgD (D:)
    gshmpepaksapapkkgskkavtkaqkkdgkkrkrsrkesysiyvykvlkqvhpdtgiss
    kamgimnsfvndiferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtk
    avtkytsak
    

    Sequence, based on observed residues (ATOM records): (download)
    >5jrgD (D:)
    kkrkrsrkesysiyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkr
    stitsreiqtavrlllpgelakhavsegtkavtkyts
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >5jrgE (E:)
    gshmartkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqk
    stellirklpfqrlvreiaqdfktdlrfqssavmalqeaceaylvglfedtnlcaihakr
    vtimpkdiqlarrirgera
    

    Sequence, based on observed residues (ATOM records): (download)
    >5jrgE (E:)
    kphryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqeac
    eaylvglfedtnlcaihakrvtimpkdiqlarrirgera
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >5jrgF (F:)
    gshmsgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrg
    vlkvflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >5jrgF (F:)
    rhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtyteha
    krktvtamdvvyalkrqgrtlygfgg
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >5jrgG (G:)
    gshmsgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavle
    yltaeilelagnaardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavll
    pkkteshhkakgk
    

    Sequence, based on observed residues (ATOM records): (download)
    >5jrgG (G:)
    arakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleyltaeilelagna
    ardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpk
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >5jrgH (H:)
    gshmpepaksapapkkgskkavtkaqkkdgkkrkrsrkesysiyvykvlkqvhpdtgiss
    kamgimnsfvndiferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtk
    avtkytsak
    

    Sequence, based on observed residues (ATOM records): (download)
    >5jrgH (H:)
    rkrsrkesysiyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkrst
    itsreiqtavrlllpgelakhavsegtkavtkytsa
    

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.