8QKT | pdb_00008qkt

Structure of a nucleosome composed of a palindromic 167-base pair blunt-ended DNA fragment


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
A [auth AAA]SCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)
E [auth EEE]SCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)
K [auth KKK]SCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)
O [auth OOO]SCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
R [auth RRR]zf-C2H2_16e8qktRRR1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: zf-C2H2_16ECOD (v294.1)
H [auth HHH]GspA_SrpA_Ne8qktHHH1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: GspA_SrpA_NECOD (v294.1)
G [auth GGG]zf-C2H2_16e8qktGGG1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: zf-C2H2_16ECOD (v294.1)
Q [auth QQQ]zf-C2H2_16e8qktQQQ1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: zf-C2H2_16ECOD (v294.1)
N [auth NNN]zf-C2H2_16e8qktNNN1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: zf-C2H2_16ECOD (v294.1)
D [auth DDD]zf-C2H2_16e8qktDDD1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: zf-C2H2_16ECOD (v294.1)
M [auth MMM]zf-C2H2_16e8qktMMM1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: zf-C2H2_16ECOD (v294.1)
C [auth CCC]zf-C2H2_16e8qktCCC1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: zf-C2H2_16ECOD (v294.1)
P [auth PPP]zf-C2H2_16e8qktPPP1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: zf-C2H2_16ECOD (v294.1)
L [auth LLL]zf-C2H2_16e8qktLLL1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: zf-C2H2_16ECOD (v294.1)
F [auth FFF]zf-C2H2_16e8qktFFF1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: zf-C2H2_16ECOD (v294.1)
B [auth BBB]zf-C2H2_16e8qktBBB1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: zf-C2H2_16ECOD (v294.1)
A [auth AAA]GspA_SrpA_Ne8qktAAA1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: GspA_SrpA_NECOD (v294.1)
E [auth EEE]zf-C2H2_16e8qktEEE1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: zf-C2H2_16ECOD (v294.1)
K [auth KKK]zf-C2H2_16e8qktKKK1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: zf-C2H2_16ECOD (v294.1)
O [auth OOO]zf-C2H2_16e8qktOOO1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: zf-C2H2_16ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
H [auth HHH],
R [auth RRR]
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
G [auth GGG],
Q [auth QQQ]
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
G [auth GGG],
Q [auth QQQ]
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
D [auth DDD],
N [auth NNN]
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
C [auth CCC],
M [auth MMM]
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
C [auth CCC],
M [auth MMM]
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
B [auth BBB],
F [auth FFF],
L [auth LLL],
P [auth PPP]
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
A [auth AAA],
E [auth EEE],
K [auth KKK],
O [auth OOO]
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
J [auth JJJ],
T [auth TTT]
DNA (167-MER)---
I [auth III],
S [auth SSS]
DNA (167-MER)---
H [auth HHH],
R [auth RRR]
Histone H2B type 1-J
G [auth GGG],
Q [auth QQQ]
Histone H2A -
D [auth DDD],
N [auth NNN]
Histone H2B type 1-J
C [auth CCC],
M [auth MMM]
Histone H2A
B [auth BBB],
F [auth FFF],
L [auth LLL],
P [auth PPP]
Histone H4 -
A [auth AAA],
E [auth EEE],
K [auth KKK],
O [auth OOO]
Histone H3.1

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
H [auth HHH],
R [auth RRR]
IPR009072Histone-foldHomologous Superfamily
H [auth HHH],
R [auth RRR]
IPR000558Histone H2BFamily
H [auth HHH],
R [auth RRR]
IPR007125Core Histone H2A/H2B/H3 domainDomain
H [auth HHH],
R [auth RRR]
IPR055333Histone H2B, conserved siteConserved Site
G [auth GGG],
Q [auth QQQ]
IPR009072Histone-foldHomologous Superfamily
G [auth GGG],
Q [auth QQQ]
IPR002119Histone H2AFamily
G [auth GGG],
Q [auth QQQ]
IPR032454Histone H2A, C-terminal domainDomain
G [auth GGG],
Q [auth QQQ]
IPR032458Histone H2A conserved siteConserved Site
G [auth GGG],
Q [auth QQQ]
IPR007125Core Histone H2A/H2B/H3 domainDomain
D [auth DDD],
N [auth NNN]
IPR009072Histone-foldHomologous Superfamily
D [auth DDD],
N [auth NNN]
IPR000558Histone H2BFamily
D [auth DDD],
N [auth NNN]
IPR007125Core Histone H2A/H2B/H3 domainDomain
D [auth DDD],
N [auth NNN]
IPR055333Histone H2B, conserved siteConserved Site
C [auth CCC],
M [auth MMM]
IPR009072Histone-foldHomologous Superfamily
C [auth CCC],
M [auth MMM]
IPR002119Histone H2AFamily
C [auth CCC],
M [auth MMM]
IPR032454Histone H2A, C-terminal domainDomain
C [auth CCC],
M [auth MMM]
IPR032458Histone H2A conserved siteConserved Site
C [auth CCC],
M [auth MMM]
IPR007125Core Histone H2A/H2B/H3 domainDomain
B [auth BBB],
F [auth FFF],
L [auth LLL],
P [auth PPP]
IPR009072Histone-foldHomologous Superfamily
B [auth BBB],
F [auth FFF],
L [auth LLL],
P [auth PPP]
IPR001951Histone H4Family
B [auth BBB],
F [auth FFF],
L [auth LLL],
P [auth PPP]
IPR035425CENP-T/Histone H4, histone foldDomain
B [auth BBB],
F [auth FFF],
L [auth LLL],
P [auth PPP]
IPR019809Histone H4, conserved siteConserved Site
B [auth BBB],
F [auth FFF],
L [auth LLL],
P [auth PPP]
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
A [auth AAA],
E [auth EEE],
K [auth KKK],
O [auth OOO]
IPR009072Histone-foldHomologous Superfamily
A [auth AAA],
E [auth EEE],
K [auth KKK],
O [auth OOO]
IPR007125Core Histone H2A/H2B/H3 domainDomain
A [auth AAA],
E [auth EEE],
K [auth KKK],
O [auth OOO]
IPR000164Histone H3/CENP-AFamily

Pharos: Disease Associations Pharos Homepage Annotation