9YLE | pdb_00009yle

State 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
L [auth H]SCOP2B SuperfamilyCore histone-like 8066283 3001387 SCOP2B (2022-06-29)
H [auth D]SCOP2B SuperfamilyCore histone-like 8066283 3001387 SCOP2B (2022-06-29)
K [auth G]SCOP2B SuperfamilyCore histone-like 8039342 3001387 SCOP2B (2022-06-29)
G [auth C]SCOP2B SuperfamilyCore histone-like 8039342 3001387 SCOP2B (2022-06-29)
J [auth F]SCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
F [auth B]SCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
I [auth E]SCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)
E [auth A]SCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)
QSCOP2B SuperfamilyDpy-30/Rlla-like 8104118 3001874 SCOP2B (2022-06-29)
PSCOP2B SuperfamilyDpy-30/Rlla-like 8104118 3001874 SCOP2B (2022-06-29)
A [auth O]SCOP2B SuperfamilyUbiquitin-like 8101457 3000157 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
G [auth C],
K [auth G]
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
F [auth B],
J [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
E [auth A],
I [auth E]
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
D [auth T]PF00622SPRY domain (SPRY)SPRY domainSPRY Domain is named from SPla and the RYanodine Receptor and it is found in many eukaryotic proteins with a wide range of functions. It is a protein-interaction module involved in many important signalling pathways like RNA processing, regulation of ...SPRY Domain is named from SPla and the RYanodine Receptor and it is found in many eukaryotic proteins with a wide range of functions. It is a protein-interaction module involved in many important signalling pathways like RNA processing, regulation of histone H3 methylation, innate immunity or embryonic development [1,2,3,4]. It can be divided into 11 subfamilies based on amino acid sequence similarity or the presence of additional protein domains. The greater SPRY family is divided into the SPRY/B30.2 (which contains a PRY extension at the N-terminal) and SPRY-only sub-families which are preceded by a subdomain that is structurally similar to the PRY region [2]. SPRY/B30.2 structures revealed a bent beta-sandwich fold comprised of two beta-sheets. Distant homologues are domains in butyrophilin/ marenostrin/pyrin [1].
Domain
C [auth N]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
B [auth K]PF00856SET domain (SET)SET domain- Family
B [auth K]PF05965F/Y rich C-terminus (FYRC)F/Y rich C-terminus- Family
B [auth K]PF05964F/Y-rich N-terminus (FYRN)F/Y-rich N-terminus- Family
B [auth K]PF13832PHD-zinc-finger like domain (zf-HC5HC2H_2)PHD-zinc-finger like domainDomain
P, Q
PF05186Dpy-30 motif (Dpy-30)Dpy-30 motif- Motif
N [auth R]PF25175WDR5 beta-propeller domain (Beta-prop_WDR5)WDR5 beta-propeller domain- Repeat
A [auth O]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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
M [auth J]DNA (145-MER)---
H [auth D],
L [auth H]
Histone H2B type 2-E
G [auth C],
K [auth G]
Histone H2A type 1-B/E
F [auth B],
J [auth F]
Histone H4
E [auth A],
I [auth E]
Histone H3.1
D [auth T]Set1/Ash2 histone methyltransferase complex subunit ASH2
C [auth N]Retinoblastoma-binding protein 5
B [auth K][histone H3]-lysine(4) N-methyltransferase,Histone-lysine N-methyltransferase 2D
P, Q
Protein dpy-30 homolog
O [auth I]DNA (145-MER)---
N [auth R]WD repeat-containing protein 5
A [auth O]Ubiquitin

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
H [auth D],
L [auth H]
IPR009072Histone-foldHomologous Superfamily
H [auth D],
L [auth H]
IPR000558Histone H2BFamily
H [auth D],
L [auth H]
IPR007125Core Histone H2A/H2B/H3 domainDomain
H [auth D],
L [auth H]
IPR055333Histone H2B, conserved siteConserved Site
G [auth C],
K [auth G]
IPR009072Histone-foldHomologous Superfamily
G [auth C],
K [auth G]
IPR002119Histone H2AFamily
G [auth C],
K [auth G]
IPR007125Core Histone H2A/H2B/H3 domainDomain
G [auth C],
K [auth G]
IPR032454Histone H2A, C-terminal domainDomain
G [auth C],
K [auth G]
IPR032458Histone H2A conserved siteConserved Site
F [auth B],
J [auth F]
IPR009072Histone-foldHomologous Superfamily
F [auth B],
J [auth F]
IPR035425CENP-T/Histone H4, histone foldDomain
F [auth B],
J [auth F]
IPR001951Histone H4Family
F [auth B],
J [auth F]
IPR019809Histone H4, conserved siteConserved Site
F [auth B],
J [auth F]
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
E [auth A],
I [auth E]
IPR009072Histone-foldHomologous Superfamily
E [auth A],
I [auth E]
IPR007125Core Histone H2A/H2B/H3 domainDomain
E [auth A],
I [auth E]
IPR000164Histone H3/CENP-AFamily
D [auth T]IPR053835Set1/Ash2 histone methyltransferase complex subunit ASH2-like, winged-helixDomain
D [auth T]IPR001870B30.2/SPRY domainDomain
D [auth T]IPR013320Concanavalin A-like lectin/glucanase domain superfamilyHomologous Superfamily
D [auth T]IPR043136B30.2/SPRY domain superfamilyHomologous Superfamily
D [auth T]IPR049455Set1/Ash2 histone methyltransferase complex subunit ASH2-like, PHD zinc fingerDomain
D [auth T]IPR037353Histone methyltransferase complex subunit ASH2Family
D [auth T]IPR003877SPRY domainDomain
C [auth N]IPR037850Retinoblastoma-binding protein 5/Swd1Family
C [auth N]IPR001680WD40 repeatRepeat
C [auth N]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
B [auth K]IPR037890KMT2D, SET domainDomain
B [auth K]IPR001965Zinc finger, PHD-typeDomain
B [auth K]IPR046341SET domain superfamilyHomologous Superfamily
B [auth K]IPR047000KMT2D, PHD3 domainDomain
B [auth K]IPR001214SET domainDomain
B [auth K]IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
B [auth K]IPR003889FY-rich, C-terminalConserved Site
B [auth K]IPR041961KMT2D, ePHD1 domainDomain
B [auth K]IPR046999KMT2D, PHD5 domainDomain
B [auth K]IPR019787Zinc finger, PHD-fingerDomain
B [auth K]IPR011011Zinc finger, FYVE/PHD-typeHomologous Superfamily
B [auth K]IPR003888FY-rich, N-terminalConserved Site
B [auth K]IPR041964KMT2D, ePHD2 domainDomain
B [auth K]IPR001841Zinc finger, RING-typeDomain
B [auth K]IPR003616Post-SET domainDomain
B [auth K]IPR034732Extended PHD (ePHD) domainDomain
B [auth K]IPR036910High mobility group box domain superfamilyHomologous Superfamily
B [auth K]IPR037890KMT2D, SET domainDomain
B [auth K]IPR001965Zinc finger, PHD-typeDomain
B [auth K]IPR046341SET domain superfamilyHomologous Superfamily
B [auth K]IPR047000KMT2D, PHD3 domainDomain
B [auth K]IPR001214SET domainDomain
B [auth K]IPR019787Zinc finger, PHD-fingerDomain
B [auth K]IPR011011Zinc finger, FYVE/PHD-typeHomologous Superfamily
B [auth K]IPR041964KMT2D, ePHD2 domainDomain
B [auth K]IPR003616Post-SET domainDomain
B [auth K]IPR034732Extended PHD (ePHD) domainDomain
B [auth K]IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
B [auth K]IPR003889FY-rich, C-terminalConserved Site
B [auth K]IPR041961KMT2D, ePHD1 domainDomain
B [auth K]IPR046999KMT2D, PHD5 domainDomain
B [auth K]IPR003888FY-rich, N-terminalConserved Site
B [auth K]IPR001841Zinc finger, RING-typeDomain
B [auth K]IPR009071High mobility group box domainDomain
B [auth K]IPR036910High mobility group box domain superfamilyHomologous Superfamily
P, Q
IPR037856Sdc1/DPY30Family
P, Q
IPR007858Dpy-30 motifConserved Site
P, Q
IPR049629DPY30/SDC1, dimerization/docking domainDomain
N [auth R]IPR059122WDR5-like, beta-propeller domainDomain
N [auth R]IPR019775WD40 repeat, conserved siteConserved Site
N [auth R]IPR020472PAC1/LIS1-like, WD-40 repeatRepeat
N [auth R]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
N [auth R]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
N [auth R]IPR001680WD40 repeatRepeat
A [auth O]IPR019954Ubiquitin conserved siteConserved Site
A [auth O]IPR050158Ubiquitin and ubiquitin-likeFamily
A [auth O]IPR000626Ubiquitin-like domainDomain
A [auth O]IPR019956Ubiquitin domainDomain
A [auth O]IPR029071Ubiquitin-like domain superfamilyHomologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
H [auth D],
L [auth H]
Q16778
G [auth C],
K [auth G]
P04908
F [auth B],
J [auth F]
P62805
E [auth A],
I [auth E]
P68431
D [auth T]Q9UBL3
C [auth N]Q15291
B [auth K]O14686
P, Q
Q9C005
N [auth R]P61964
A [auth O]P0CG47