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.