7BWD | pdb_00007bwd

Structure of Dot1L-H2BK34ub Nucleosome Complex


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
F [auth A]SCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)
G [auth D]SCOP2B SuperfamilyCore histone-like 8039341 3001387 SCOP2B (2022-06-29)
D [auth H]SCOP2B SuperfamilyCore histone-like 8039341 3001387 SCOP2B (2022-06-29)
H [auth C]SCOP2B SuperfamilyCore histone-like 8039342 3001387 SCOP2B (2022-06-29)
C [auth G]SCOP2B SuperfamilyCore histone-like 8039342 3001387 SCOP2B (2022-06-29)
I [auth B]SCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
B [auth F]SCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
A [auth K]SCOP2B SuperfamilyS-adenosyl-L-methionine-dependent methyltransferases 8033656 3000118 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
Mubiquitin_1e7bwdM1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Ubiquitin-likeF: ubiquitin_1ECOD (1.6)
Lubiquitin_1e7bwdL1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Ubiquitin-likeF: ubiquitin_1ECOD (1.6)
F [auth A]Histonee7bwdA1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: HistoneECOD (1.6)
EHistonee7bwdE1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: HistoneECOD (1.6)
G [auth D]Histonee7bwdD1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: HistoneECOD (1.6)
D [auth H]Histonee7bwdH1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: HistoneECOD (1.6)
H [auth C]Histone_1e7bwdC1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: Histone_1ECOD (1.6)
C [auth G]Histone_1e7bwdG1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: Histone_1ECOD (1.6)
I [auth B]Histone_1e7bwdB1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: Histone_1ECOD (1.6)
B [auth F]Histone_1e7bwdF1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: Histone_1ECOD (1.6)
A [auth K]DOT1e7bwdK1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: S-adenosyl-L-methionine-dependent methyltransferasesF: DOT1ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
L, M
PF00240Ubiquitin family (ubiquitin)Ubiquitin familyThis family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].
Domain
C [auth G],
H [auth C]
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
B [auth F],
I [auth B]
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 K]PF08123Histone methylation protein DOT1 (DOT1)Histone methylation protein DOT1The DOT1 domain regulates gene expression by methylating histone H3 [1]. H3 methylation by DOT1 has been shown to be required for the DNA damage checkpoint in yeast [2]. Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
L, M
Ubiquitin
K [auth J]DNA (146-MER)---
J [auth I]DNA (146-MER)---
E,
F [auth A]
Histone H3.1
D [auth H],
G [auth D]
Histone H2B type 1-K
C [auth G],
H [auth C]
Histone H2A type 1-B/E
B [auth F],
I [auth B]
Histone H4
A [auth K]Histone-lysine N-methyltransferase, H3 lysine-79 specific

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
L, M
IPR019954Ubiquitin conserved siteConserved Site
L, M
IPR038582Small ribosomal subunit protein eS31 eukaryotic superfamilyHomologous Superfamily
L, M
IPR050158Ubiquitin and ubiquitin-likeFamily
L, M
IPR011332Zinc-binding ribosomal proteinHomologous Superfamily
L, M
IPR000626Ubiquitin-like domainDomain
L, M
IPR002906Small ribosomal subunit protein eS31Domain
L, M
IPR019956Ubiquitin domainDomain
L, M
IPR029071Ubiquitin-like domain superfamilyHomologous Superfamily
E,
F [auth A]
IPR009072Histone-foldHomologous Superfamily
E,
F [auth A]
IPR007125Core Histone H2A/H2B/H3 domainDomain
E,
F [auth A]
IPR000164Histone H3/CENP-AFamily
D [auth H],
G [auth D]
IPR009072Histone-foldHomologous Superfamily
D [auth H],
G [auth D]
IPR000558Histone H2BFamily
D [auth H],
G [auth D]
IPR007125Core Histone H2A/H2B/H3 domainDomain
D [auth H],
G [auth D]
IPR055333Histone H2B, conserved siteConserved Site
C [auth G],
H [auth C]
IPR009072Histone-foldHomologous Superfamily
C [auth G],
H [auth C]
IPR002119Histone H2AFamily
C [auth G],
H [auth C]
IPR007125Core Histone H2A/H2B/H3 domainDomain
C [auth G],
H [auth C]
IPR032454Histone H2A, C-terminal domainDomain
C [auth G],
H [auth C]
IPR032458Histone H2A conserved siteConserved Site
B [auth F],
I [auth B]
IPR009072Histone-foldHomologous Superfamily
B [auth F],
I [auth B]
IPR035425CENP-T/Histone H4, histone foldDomain
B [auth F],
I [auth B]
IPR001951Histone H4Family
B [auth F],
I [auth B]
IPR019809Histone H4, conserved siteConserved Site
B [auth F],
I [auth B]
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
A [auth K]IPR030445Histone H3-K79 methyltransferaseFamily
A [auth K]IPR029063S-adenosyl-L-methionine-dependent methyltransferase superfamilyHomologous Superfamily
A [auth K]IPR025789Histone-lysine N-methyltransferase DOT1 domainDomain
A [auth K]IPR021169Histone H3-K79 methyltransferase, metazoaFamily

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
L, M
PharosP62979
E,
F [auth A]
PharosP68431
D [auth H],
G [auth D]
PharosO60814
C [auth G],
H [auth C]
PharosP04908
B [auth F],
I [auth B]
PharosP62805
A [auth K]PharosQ8TEK3