PDB entry 5y0c
View 5y0c on RCSB PDB site
Description: Crystal Structure of the human nucleosome at 2.09 angstrom resolution
Class: DNA binding protein/DNA
Keywords: DNA binding, nucleus, histone fold, chromatin formation, nucleosome, DNA BINDING PROTEIN-DNA complex
Deposited on
2017-07-16, released
2018-07-18
The last revision prior to the SCOPe 2.07 freeze date was dated
2018-07-18, with a file datestamp of
2018-07-13.
Experiment type: XRAY
Resolution: 2.09 Å
R-factor: N/A
AEROSPACI score: 0.3
(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: d5y0cb_ - 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: d5y0cc_ - 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: d5y0cd_ - 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: d5y0cf_ - 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: d5y0cg_ - Chain 'H':
Compound: Histone H2B type 1-J
Species: Homo sapiens [TaxId:9606]
Gene: HIST1H2BJ, H2BFR
Database cross-references and differences (RAF-indexed):
- Chain 'I':
Compound: DNA (146-mer)
Species: Homo sapiens [TaxId:9606]
- Chain 'J':
Compound: DNA (146-mer)
Species: Homo sapiens [TaxId:9606]
- Heterogens: MN, CL, HOH
PDB Chain Sequences:
- Chain 'A':
No sequence available.
- Chain 'B':
Sequence, based on SEQRES records: (download)
>5y0cB (B:)
gshmsgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrg
vlkvflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg
Sequence, based on observed residues (ATOM records): (download)
>5y0cB (B:)
niqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrktvtam
dvvyalkrqgrtlygfg
- Chain 'C':
Sequence, based on SEQRES records: (download)
>5y0cC (C:)
gshmsgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavle
yltaeilelagnaardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavll
pkkteshhkakgk
Sequence, based on observed residues (ATOM records): (download)
>5y0cC (C:)
rakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleyltaeilelagnaa
rdnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpk
- Chain 'D':
Sequence, based on SEQRES records: (download)
>5y0cD (D:)
gshmpepaksapapkkgskkavtkaqkkdgkkrkrsrkesysiyvykvlkqvhpdtgiss
kamgimnsfvndiferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtk
avtkytsak
Sequence, based on observed residues (ATOM records): (download)
>5y0cD (D:)
srkesysiyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkrstits
reiqtavrlllpgelakhavsegtkavtkyts
- Chain 'E':
No sequence available.
- Chain 'F':
Sequence, based on SEQRES records: (download)
>5y0cF (F:)
gshmsgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrg
vlkvflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg
Sequence, based on observed residues (ATOM records): (download)
>5y0cF (F:)
krhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtyteh
akrktvtamdvvyalkrqgrtlygfgg
- Chain 'G':
Sequence, based on SEQRES records: (download)
>5y0cG (G:)
gshmsgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavle
yltaeilelagnaardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavll
pkkteshhkakgk
Sequence, based on observed residues (ATOM records): (download)
>5y0cG (G:)
ktrssraglqfpvgrvhrllrkgnyservgagapvylaavleyltaeilelagnaardnk
ktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpk
- Chain 'H':
No sequence available.
- Chain 'I':
No sequence available.
- Chain 'J':
No sequence available.