PDB entry 6kvd

View 6kvd on RCSB PDB site
Description: Crystal structure of human nucleosome containing H2A.J
Class: DNA binding protein/DNA
Keywords: nucleosome, histone variant, chromatin, DNA BINDING PROTEIN-DNA complex
Deposited on 2019-09-04, released 2019-12-18
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-04-08, with a file datestamp of 2020-04-03.
Experiment type: XRAY
Resolution: 2.21 Å
R-factor: N/A
AEROSPACI score: 0.26 (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 2.08: d6kvdb_
  • Chain 'C':
    Compound: Histone H2A.J
    Species: Homo sapiens [TaxId:9606]
    Gene: H2AFJ
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6kvdc_
  • 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 2.08: d6kvdd_
  • 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 2.08: d6kvdf_
  • Chain 'G':
    Compound: Histone H2A.J
    Species: Homo sapiens [TaxId:9606]
    Gene: H2AFJ
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6kvdg_
  • 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 2.08: d6kvdh_
  • Chain 'I':
    Compound: DNA (146-mer)
    Species: Homo sapiens [TaxId:9606]
  • Chain 'J':
    Compound: DNA (146-mer)
    Species: Homo sapiens [TaxId:9606]
  • Heterogens: CL, MN, HOH

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

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

    Sequence, based on observed residues (ATOM records): (download) 
    >6kvdB (B:)
niqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrktvtam
dvvyalkrqgrtlygfg

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6kvdC (C:)
gshmsgrgkqggkvrakaksrssraglqfpvgrvhrllrkgnyaervgagapvylaavle
yltaeilelagnaardnkktriiprhlqlairndeelnkllgkvtiaqggvlpniqavll
pkktesqktksk

    Sequence, based on observed residues (ATOM records): (download) 
    >6kvdC (C:)
rakaksrssraglqfpvgrvhrllrkgnyaervgagapvylaavleyltaeilelagnaa
rdnkktriiprhlqlairndeelnkllgkvtiaqggvlpniqavllp

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

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

  • Chain 'E':
    No sequence available.

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

    Sequence, based on observed residues (ATOM records): (download) 
    >6kvdF (F:)
hrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehak
rktvtamdvvyalkrqgrtlygfgg

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >6kvdG (G:)
gshmsgrgkqggkvrakaksrssraglqfpvgrvhrllrkgnyaervgagapvylaavle
yltaeilelagnaardnkktriiprhlqlairndeelnkllgkvtiaqggvlpniqavll
pkktesqktksk

    Sequence, based on observed residues (ATOM records): (download) 
    >6kvdG (G:)
aksrssraglqfpvgrvhrllrkgnyaervgagapvylaavleyltaeilelagnaardn
kktriiprhlqlairndeelnkllgkvtiaqggvlpniqavllpk

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

    Sequence, based on observed residues (ATOM records): (download) 
    >6kvdH (H:)
srkesysiyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkrstits
reiqtavrlllpgelakhavsegtkavtkyts

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.