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8GRM

Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome

Functional Information from GO Data
ChainGOidnamespacecontents
A0000786cellular_componentnucleosome
A0003677molecular_functionDNA binding
A0030527molecular_functionstructural constituent of chromatin
A0046982molecular_functionprotein heterodimerization activity
B0003677molecular_functionDNA binding
B0030527molecular_functionstructural constituent of chromatin
B0046982molecular_functionprotein heterodimerization activity
C0000786cellular_componentnucleosome
C0003677molecular_functionDNA binding
C0030527molecular_functionstructural constituent of chromatin
C0046982molecular_functionprotein heterodimerization activity
D0000786cellular_componentnucleosome
D0003677molecular_functionDNA binding
D0030527molecular_functionstructural constituent of chromatin
D0046982molecular_functionprotein heterodimerization activity
E0000786cellular_componentnucleosome
E0003677molecular_functionDNA binding
E0030527molecular_functionstructural constituent of chromatin
E0046982molecular_functionprotein heterodimerization activity
F0003677molecular_functionDNA binding
F0030527molecular_functionstructural constituent of chromatin
F0046982molecular_functionprotein heterodimerization activity
G0000786cellular_componentnucleosome
G0003677molecular_functionDNA binding
G0030527molecular_functionstructural constituent of chromatin
G0046982molecular_functionprotein heterodimerization activity
H0000786cellular_componentnucleosome
H0003677molecular_functionDNA binding
H0030527molecular_functionstructural constituent of chromatin
H0046982molecular_functionprotein heterodimerization activity
N0000151cellular_componentubiquitin ligase complex
P0000151cellular_componentubiquitin ligase complex
P0000209biological_processprotein polyubiquitination
P0004842molecular_functionubiquitin-protein transferase activity
P0005515molecular_functionprotein binding
P0005524molecular_functionATP binding
P0005634cellular_componentnucleus
P0005654cellular_componentnucleoplasm
P0005829cellular_componentcytosol
P0006511biological_processubiquitin-dependent protein catabolic process
P0016567biological_processprotein ubiquitination
P0016740molecular_functiontransferase activity
P0019787molecular_functionubiquitin-like protein transferase activity
P0031625molecular_functionubiquitin protein ligase binding
P0032991cellular_componentprotein-containing complex
P0036211biological_processprotein modification process
P0051865biological_processprotein autoubiquitination
P0061630molecular_functionubiquitin protein ligase activity
P0061631molecular_functionubiquitin conjugating enzyme activity
P0070062cellular_componentextracellular exosome
P0070936biological_processprotein K48-linked ubiquitination
Functional Information from PROSITE/UniProt
site_idPS00183
Number of Residues16
DetailsUBC_1 Ubiquitin-conjugating (UBC) active site signature. YHPNInsn.GsICLdiL
ChainResidueDetails
PTYR74-LEU89

site_idPS00357
Number of Residues23
DetailsHISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG
ChainResidueDetails
HARG92-GLY114
DARG92-GLY114

site_idPS00959
Number of Residues9
DetailsHISTONE_H3_2 Histone H3 signature 2. PFqRLVREI
ChainResidueDetails
APRO66-ILE74

site_idPS00299
Number of Residues26
DetailsUBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
ChainResidueDetails
OLYS27-ASP52

site_idPS00046
Number of Residues7
DetailsHISTONE_H2A Histone H2A signature. AGLqFPV
ChainResidueDetails
CALA21-VAL27

site_idPS00518
Number of Residues10
DetailsZF_RING_1 Zinc finger RING-type signature. ClHsFCktCI
ChainResidueDetails
MCYS34-ILE43
NCYS67-LEU76

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsACT_SITE: Glycyl thioester intermediate => ECO:0000255|PROSITE-ProRule:PRU00388, ECO:0000255|PROSITE-ProRule:PRU10133
ChainResidueDetails
HLYS120
PCYS85
FLYS20

site_idSWS_FT_FI2
Number of Residues6
DetailsMOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435
ChainResidueDetails
BLYS91
FLYS31
FLYS77
FLYS91
BLYS77
BLYS31

site_idSWS_FT_FI3
Number of Residues2
DetailsMOD_RES: N6-propionyllysine; alternate => ECO:0000269|PubMed:17267393
ChainResidueDetails
GLYS74
GLYS75
BLYS44
FLYS44

site_idSWS_FT_FI4
Number of Residues2
DetailsMOD_RES: Phosphoserine; by PAK2 => ECO:0000269|PubMed:21724829, ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569
ChainResidueDetails
FSER47
BSER47

site_idSWS_FT_FI5
Number of Residues2
DetailsMOD_RES: Phosphotyrosine => ECO:0007744|PubMed:15592455, ECO:0007744|PubMed:20068231
ChainResidueDetails
BTYR51
FTYR51

site_idSWS_FT_FI6
Number of Residues2
DetailsMOD_RES: N6-glutaryllysine; alternate => ECO:0000269|PubMed:31542297
ChainResidueDetails
GLYS118
GLYS119
FLYS59
BLYS59

site_idSWS_FT_FI7
Number of Residues2
DetailsMOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P62806
ChainResidueDetails
BLYS79
FLYS79

site_idSWS_FT_FI8
Number of Residues2
DetailsMOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P62806
ChainResidueDetails
GLYS119
BTHR80
FTHR80

site_idSWS_FT_FI9
Number of Residues2
DetailsMOD_RES: Phosphotyrosine => ECO:0007744|PubMed:24275569
ChainResidueDetails
BTYR88
FTYR88

site_idSWS_FT_FI10
Number of Residues6
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:28112733
ChainResidueDetails
BLYS59
BLYS79
FLYS20
FLYS59
FLYS79
BLYS20

site_idSWS_FT_FI11
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:19818714
ChainResidueDetails
BLYS91
FLYS91
ALYS122

site_idSWS_FT_FI12
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate => ECO:0000269|PubMed:30886146
ChainResidueDetails
BLYS31
FLYS31

221051

PDB entries from 2024-06-12

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