8G57 | pdb_00008g57

Structure of nucleosome-bound Sirtuin 6 deacetylase


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
H [auth G]SCOP2B SuperfamilyCore histone-like 8039342 3001387 SCOP2B (2022-06-29)
D [auth C]SCOP2B SuperfamilyCore histone-like 8039342 3001387 SCOP2B (2022-06-29)
G [auth F]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
C [auth B]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
F [auth E]SCOP2B SuperfamilyCore histone-like 8041272 3001387 SCOP2B (2022-06-29)
B [auth A]SCOP2B SuperfamilyCore histone-like 8041272 3001387 SCOP2B (2022-06-29)
A [auth K]SCOP2B SuperfamilyDHS-like NAD/FAD-binding domain 8063732 3001728 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
I [auth H]F_UNCLASSIFIEDe8g57H1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: F_UNCLASSIFIEDECOD (1.6)
E [auth D]F_UNCLASSIFIEDe8g57D1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: F_UNCLASSIFIEDECOD (1.6)
H [auth G]F_UNCLASSIFIEDe8g57G1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: F_UNCLASSIFIEDECOD (1.6)
D [auth C]F_UNCLASSIFIEDe8g57C1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: F_UNCLASSIFIEDECOD (1.6)
G [auth F]F_UNCLASSIFIEDe8g57F1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: F_UNCLASSIFIEDECOD (1.6)
C [auth B]F_UNCLASSIFIEDe8g57B1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: F_UNCLASSIFIEDECOD (1.6)
F [auth E]F_UNCLASSIFIEDe8g57E1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: F_UNCLASSIFIEDECOD (1.6)
B [auth A]F_UNCLASSIFIEDe8g57A1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: F_UNCLASSIFIEDECOD (1.6)
A [auth K]F_UNCLASSIFIEDe8g57K2 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: DHS-like NAD/FAD-binding domainF: F_UNCLASSIFIEDECOD (1.6)
A [auth K]F_UNCLASSIFIEDe8g57K1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: F_UNCLASSIFIEDECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
D [auth C],
H [auth G]
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
C [auth B],
G [auth F]
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
B [auth A],
F [auth E]
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
K [auth J]DNA strand 2---
J [auth I]DNA strand 1---
E [auth D],
I [auth H]
Histone H2B type 1-J
D [auth C],
H [auth G]
Histone H2A type 1-B/E
C [auth B],
G [auth F]
Histone H4
B [auth A],
F [auth E]
Histone H3 -
A [auth K]NAD-dependent protein deacylase sirtuin-6