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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

9V9Q

Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome

Functional Information from GO Data
ChainGOidnamespacecontents
A0000786cellular_componentnucleosome
A0005634cellular_componentnucleus
A0005694cellular_componentchromosome
A0006334biological_processnucleosome assembly
A0030527molecular_functionstructural constituent of chromatin
B0000786cellular_componentnucleosome
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005694cellular_componentchromosome
B0006334biological_processnucleosome assembly
B0030527molecular_functionstructural constituent of chromatin
B0031507biological_processheterochromatin formation
C0000786cellular_componentnucleosome
C0005634cellular_componentnucleus
C0005694cellular_componentchromosome
C0030527molecular_functionstructural constituent of chromatin
C0031507biological_processheterochromatin formation
D0000786cellular_componentnucleosome
D0002227biological_processinnate immune response in mucosa
D0003677molecular_functionDNA binding
D0005576cellular_componentextracellular region
D0005634cellular_componentnucleus
D0005694cellular_componentchromosome
D0006325biological_processchromatin organization
D0019731biological_processantibacterial humoral response
D0030527molecular_functionstructural constituent of chromatin
D0061844biological_processantimicrobial humoral immune response mediated by antimicrobial peptide
E0000786cellular_componentnucleosome
E0005634cellular_componentnucleus
E0005694cellular_componentchromosome
E0006334biological_processnucleosome assembly
E0030527molecular_functionstructural constituent of chromatin
F0000786cellular_componentnucleosome
F0005515molecular_functionprotein binding
F0005634cellular_componentnucleus
F0005694cellular_componentchromosome
F0006334biological_processnucleosome assembly
F0030527molecular_functionstructural constituent of chromatin
F0031507biological_processheterochromatin formation
G0000786cellular_componentnucleosome
G0005634cellular_componentnucleus
G0005694cellular_componentchromosome
G0030527molecular_functionstructural constituent of chromatin
G0031507biological_processheterochromatin formation
H0000786cellular_componentnucleosome
H0002227biological_processinnate immune response in mucosa
H0003677molecular_functionDNA binding
H0005576cellular_componentextracellular region
H0005634cellular_componentnucleus
H0005694cellular_componentchromosome
H0006325biological_processchromatin organization
H0019731biological_processantibacterial humoral response
H0030527molecular_functionstructural constituent of chromatin
H0061844biological_processantimicrobial humoral immune response mediated by antimicrobial peptide
M0000122biological_processnegative regulation of transcription by RNA polymerase II
M0000151cellular_componentubiquitin ligase complex
M0000785cellular_componentchromatin
M0000792cellular_componentheterochromatin
M0003682molecular_functionchromatin binding
M0005515molecular_functionprotein binding
M0005634cellular_componentnucleus
M0005654cellular_componentnucleoplasm
M0005737cellular_componentcytoplasm
M0006338biological_processchromatin remodeling
M0007379biological_processsegment specification
M0008270molecular_functionzinc ion binding
M0010468biological_processregulation of gene expression
M0016604cellular_componentnuclear body
M0030097biological_processhemopoiesis
M0030890biological_processpositive regulation of B cell proliferation
M0031507biological_processheterochromatin formation
M0031519cellular_componentPcG protein complex
M0033092biological_processpositive regulation of immature T cell proliferation in thymus
M0035102cellular_componentPRC1 complex
M0045814biological_processnegative regulation of gene expression, epigenetic
M0045892biological_processnegative regulation of DNA-templated transcription
M0048146biological_processpositive regulation of fibroblast proliferation
M0051443biological_processpositive regulation of ubiquitin-protein transferase activity
M0071535molecular_functionRING-like zinc finger domain binding
M0097027molecular_functionubiquitin-protein transferase activator activity
M1990841molecular_functionpromoter-specific chromatin binding
N0000122biological_processnegative regulation of transcription by RNA polymerase II
N0000151cellular_componentubiquitin ligase complex
N0000785cellular_componentchromatin
N0000791cellular_componenteuchromatin
N0000792cellular_componentheterochromatin
N0001739cellular_componentsex chromatin
N0003682molecular_functionchromatin binding
N0004842molecular_functionubiquitin-protein transferase activity
N0005515molecular_functionprotein binding
N0005634cellular_componentnucleus
N0005654cellular_componentnucleoplasm
N0005694cellular_componentchromosome
N0005737cellular_componentcytoplasm
N0006338biological_processchromatin remodeling
N0007281biological_processgerm cell development
N0008270molecular_functionzinc ion binding
N0016567biological_processprotein ubiquitination
N0016604cellular_componentnuclear body
N0031507biological_processheterochromatin formation
N0031519cellular_componentPcG protein complex
N0035102cellular_componentPRC1 complex
N0040029biological_processepigenetic regulation of gene expression
N0045892biological_processnegative regulation of DNA-templated transcription
N0045893biological_processpositive regulation of DNA-templated transcription
N0061630molecular_functionubiquitin protein ligase activity
N0071339cellular_componentMLL1 complex
N0071535molecular_functionRING-like zinc finger domain binding
N0140862molecular_functionhistone H2AK119 ubiquitin ligase activity
N1990904cellular_componentribonucleoprotein complex
P0000122biological_processnegative regulation of transcription by RNA polymerase II
P0000209biological_processprotein polyubiquitination
P0004842molecular_functionubiquitin-protein transferase activity
P0005515molecular_functionprotein binding
P0005654cellular_componentnucleoplasm
P0005737cellular_componentcytoplasm
P0005829cellular_componentcytosol
P0005886cellular_componentplasma membrane
P0006511biological_processubiquitin-dependent protein catabolic process
P0006513biological_processprotein monoubiquitination
P0010008cellular_componentendosome membrane
P0016567biological_processprotein ubiquitination
P0030514biological_processnegative regulation of BMP signaling pathway
P0036211biological_processprotein modification process
P0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
P0051865biological_processprotein autoubiquitination
P0061630molecular_functionubiquitin protein ligase activity
P0061631molecular_functionubiquitin conjugating enzyme activity
P0070062cellular_componentextracellular exosome
P0070936biological_processprotein K48-linked ubiquitination
P0070979biological_processprotein K11-linked ubiquitination
P0085020biological_processprotein K6-linked ubiquitination
P1903749biological_processpositive regulation of protein localization to mitochondrion
Functional Information from PROSITE/UniProt
site_idPS00046
Number of Residues7
DetailsHISTONE_H2A Histone H2A signature. AGLqFPV
ChainResidueDetails
CALA21-VAL27
site_idPS00047
Number of Residues5
DetailsHISTONE_H4 Histone H4 signature. GAKRH
ChainResidueDetails
BGLY14-HIS18
site_idPS00299
Number of Residues26
DetailsUBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
ChainResidueDetails
OLYS27-ASP52
RLYS27-ASP52
site_idPS00322
Number of Residues7
DetailsHISTONE_H3_1 Histone H3 signature 1. KAPRKQL
ChainResidueDetails
ALYS14-LEU20
site_idPS00357
Number of Residues23
DetailsHISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG
ChainResidueDetails
DARG89-GLY111
site_idPS00518
Number of Residues10
DetailsZF_RING_1 Zinc finger RING-type signature. ClHrFCadCI
ChainResidueDetails
NCYS67-ILE76
MCYS34-ILE43
site_idPS00959
Number of Residues9
DetailsHISTONE_H3_2 Histone H3 signature 2. PFqRLVREI
ChainResidueDetails
APRO66-ILE74
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI2
Number of Residues1
DetailsModified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues4
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues4
DetailsModified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine; by PAK2","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues4
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues2
DetailsModified residue: {"description":"N6-methacryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues2
DetailsModified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues79
DetailsZinc finger: {"description":"RING-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00175","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues14
DetailsMotif: {"description":"Nuclear localization signal","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues5
DetailsRegion: {"description":"Interaction with nucleosomes via an acidic patch on histone H2A and histone H2B","evidences":[{"source":"PubMed","id":"25355358","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"25519132","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI15
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"Q9CQJ4","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI16
Number of Residues1
DetailsActive site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10133","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI17
Number of Residues75
DetailsDomain: {"description":"Ubiquitin-like","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI18
Number of Residues2
DetailsSite: {"description":"Interacts with activating enzyme"}
ChainResidueDetails
site_idSWS_FT_FI19
Number of Residues1
DetailsSite: {"description":"Essential for function"}
ChainResidueDetails
site_idSWS_FT_FI20
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine; by PINK1","evidences":[{"source":"PubMed","id":"24660806","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24751536","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24784582","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25527291","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI21
Number of Residues1
DetailsModified residue: {"description":"(Microbial infection) ADP-ribosylthreonine","evidences":[{"source":"PubMed","id":"32330457","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI22
Number of Residues1
DetailsModified residue: {"description":"ADP-ribosylglycine","evidences":[{"source":"PubMed","id":"28525742","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI23
Number of Residues1
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16443603","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI24
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)"}
ChainResidueDetails
site_idSWS_FT_FI25
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16443603","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI26
Number of Residues1
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"15466860","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI27
Number of Residues1
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752573","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34239127","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI28
Number of Residues1
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI29
Number of Residues1
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18719106","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

258009

PDB entries from 2026-08-12

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