9BE6 | pdb_00009be6

Cryo-EM structure of Human Nucleosome collected by Leginon on Krios at 3.0 Angstrom resolution


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ESCOP2B SuperfamilyCore histone-like 8070531 3001387 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyCore histone-like 8039342 3001387 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyCore histone-like 8067130 3001387 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyCore histone-like 8070531 3001387 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
PF15511Centromere kinetochore component CENP-T histone fold (CENP-T_C)Centromere kinetochore component CENP-T histone foldCENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].
Domain
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
PF15511Centromere kinetochore component CENP-T histone fold (CENP-T_C)Centromere kinetochore component CENP-T histone foldCENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].
Domain
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Histone H2B type 1-J
Histone H3.2
Histone H4
DNA (145-MER)---
Histone H2B type 1-J
Histone H2A type 1-B/E
Histone H2A type 1
Histone H4 -
DNA (145-MER)---
Histone H3.2

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR009072Histone-foldHomologous Superfamily
IPR000558Histone H2BFamily
IPR007125Core Histone H2A/H2B/H3 domainDomain
IPR055333Histone H2B, conserved siteConserved Site
IPR009072Histone-foldHomologous Superfamily
IPR007125Core Histone H2A/H2B/H3 domainDomain
IPR000164Histone H3/CENP-AFamily
IPR009072Histone-foldHomologous Superfamily
IPR035425CENP-T/Histone H4, histone foldDomain
IPR001951Histone H4Family
IPR019809Histone H4, conserved siteConserved Site
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
IPR009072Histone-foldHomologous Superfamily
IPR000558Histone H2BFamily
IPR007125Core Histone H2A/H2B/H3 domainDomain
IPR055333Histone H2B, conserved siteConserved Site
IPR009072Histone-foldHomologous Superfamily
IPR002119Histone H2AFamily
IPR007125Core Histone H2A/H2B/H3 domainDomain
IPR032454Histone H2A, C-terminal domainDomain
IPR032458Histone H2A conserved siteConserved Site
IPR009072Histone-foldHomologous Superfamily
IPR002119Histone H2AFamily
IPR007125Core Histone H2A/H2B/H3 domainDomain
IPR032454Histone H2A, C-terminal domainDomain
IPR032458Histone H2A conserved siteConserved Site
IPR009072Histone-foldHomologous Superfamily
IPR001951Histone H4Family
IPR035425CENP-T/Histone H4, histone foldDomain
IPR019809Histone H4, conserved siteConserved Site
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
IPR009072Histone-foldHomologous Superfamily
IPR007125Core Histone H2A/H2B/H3 domainDomain
IPR000164Histone H3/CENP-AFamily

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
PharosP06899
PharosQ71DI3
PharosP62805
PharosP06899
PharosP04908
PharosP0C0S8
PharosQ71DI3