Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

9V9Y

Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 and one RYBP bound to the H2AK119ub-modified nucleosome

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000786	cellular_component	nucleosome
A	0005634	cellular_component	nucleus
A	0005694	cellular_component	chromosome
A	0006334	biological_process	nucleosome assembly
A	0030527	molecular_function	structural constituent of chromatin
B	0000786	cellular_component	nucleosome
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005694	cellular_component	chromosome
B	0006334	biological_process	nucleosome assembly
B	0030527	molecular_function	structural constituent of chromatin
B	0031507	biological_process	heterochromatin formation
C	0000786	cellular_component	nucleosome
C	0005634	cellular_component	nucleus
C	0005694	cellular_component	chromosome
C	0030527	molecular_function	structural constituent of chromatin
C	0031507	biological_process	heterochromatin formation
D	0000786	cellular_component	nucleosome
D	0002227	biological_process	innate immune response in mucosa
D	0003677	molecular_function	DNA binding
D	0005576	cellular_component	extracellular region
D	0005634	cellular_component	nucleus
D	0005694	cellular_component	chromosome
D	0006325	biological_process	chromatin organization
D	0019731	biological_process	antibacterial humoral response
D	0030527	molecular_function	structural constituent of chromatin
D	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
E	0000786	cellular_component	nucleosome
E	0005634	cellular_component	nucleus
E	0005694	cellular_component	chromosome
E	0006334	biological_process	nucleosome assembly
E	0030527	molecular_function	structural constituent of chromatin
F	0000786	cellular_component	nucleosome
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005694	cellular_component	chromosome
F	0006334	biological_process	nucleosome assembly
F	0030527	molecular_function	structural constituent of chromatin
F	0031507	biological_process	heterochromatin formation
G	0000786	cellular_component	nucleosome
G	0005634	cellular_component	nucleus
G	0005694	cellular_component	chromosome
G	0030527	molecular_function	structural constituent of chromatin
G	0031507	biological_process	heterochromatin formation
H	0000786	cellular_component	nucleosome
H	0002227	biological_process	innate immune response in mucosa
H	0003677	molecular_function	DNA binding
H	0005576	cellular_component	extracellular region
H	0005634	cellular_component	nucleus
H	0005694	cellular_component	chromosome
H	0006325	biological_process	chromatin organization
H	0019731	biological_process	antibacterial humoral response
H	0030527	molecular_function	structural constituent of chromatin
H	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
L	0000785	cellular_component	chromatin
L	0003676	molecular_function	nucleic acid binding
L	0003677	molecular_function	DNA binding
L	0003712	molecular_function	transcription coregulator activity
L	0003714	molecular_function	transcription corepressor activity
L	0005515	molecular_function	protein binding
L	0005634	cellular_component	nucleus
L	0005654	cellular_component	nucleoplasm
L	0005737	cellular_component	cytoplasm
L	0006338	biological_process	chromatin remodeling
L	0006355	biological_process	regulation of DNA-templated transcription
L	0031507	biological_process	heterochromatin formation
L	0031519	cellular_component	PcG protein complex
L	0032435	biological_process	negative regulation of proteasomal ubiquitin-dependent protein catabolic process
L	0035102	cellular_component	PRC1 complex
L	0043065	biological_process	positive regulation of apoptotic process
L	0045892	biological_process	negative regulation of DNA-templated transcription
L	0045893	biological_process	positive regulation of DNA-templated transcription
M	0000122	biological_process	negative regulation of transcription by RNA polymerase II
M	0000151	cellular_component	ubiquitin ligase complex
M	0000785	cellular_component	chromatin
M	0005515	molecular_function	protein binding
M	0005634	cellular_component	nucleus
M	0005654	cellular_component	nucleoplasm
M	0005737	cellular_component	cytoplasm
M	0006338	biological_process	chromatin remodeling
M	0007379	biological_process	segment specification
M	0008270	molecular_function	zinc ion binding
M	0010468	biological_process	regulation of gene expression
M	0030097	biological_process	hemopoiesis
M	0030890	biological_process	positive regulation of B cell proliferation
M	0031507	biological_process	heterochromatin formation
M	0031519	cellular_component	PcG protein complex
M	0033092	biological_process	positive regulation of immature T cell proliferation in thymus
M	0035102	cellular_component	PRC1 complex
M	0045814	biological_process	negative regulation of gene expression, epigenetic
M	0045892	biological_process	negative regulation of DNA-templated transcription
M	0048146	biological_process	positive regulation of fibroblast proliferation
M	0051443	biological_process	positive regulation of ubiquitin-protein transferase activity
M	0071535	molecular_function	RING-like zinc finger domain binding
M	1990841	molecular_function	promoter-specific chromatin binding
N	0000122	biological_process	negative regulation of transcription by RNA polymerase II
N	0000151	cellular_component	ubiquitin ligase complex
N	0000785	cellular_component	chromatin
N	0003682	molecular_function	chromatin binding
N	0004842	molecular_function	ubiquitin-protein transferase activity
N	0005515	molecular_function	protein binding
N	0005634	cellular_component	nucleus
N	0005654	cellular_component	nucleoplasm
N	0005694	cellular_component	chromosome
N	0005737	cellular_component	cytoplasm
N	0006338	biological_process	chromatin remodeling
N	0007281	biological_process	germ cell development
N	0008270	molecular_function	zinc ion binding
N	0016567	biological_process	protein ubiquitination
N	0016604	cellular_component	nuclear body
N	0031507	biological_process	heterochromatin formation
N	0031519	cellular_component	PcG protein complex
N	0035102	cellular_component	PRC1 complex
N	0040029	biological_process	epigenetic regulation of gene expression
N	0045892	biological_process	negative regulation of DNA-templated transcription
N	0045893	biological_process	positive regulation of DNA-templated transcription
N	0061630	molecular_function	ubiquitin protein ligase activity
N	0071339	cellular_component	MLL1 complex
N	0071535	molecular_function	RING-like zinc finger domain binding
N	0140862	molecular_function	histone H2AK119 ubiquitin ligase activity

Functional Information from PROSITE/UniProt

site_id	PS00046
Number of Residues	7
Details	HISTONE_H2A Histone H2A signature. AGLqFPV

Chain	Residue	Details
C	ALA21-VAL27

site_id	PS00047
Number of Residues	5
Details	HISTONE_H4 Histone H4 signature. GAKRH

Chain	Residue	Details
B	GLY14-HIS18

site_id	PS00299
Number of Residues	26
Details	UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD

Chain	Residue	Details
K	LYS27-ASP52

site_id	PS00322
Number of Residues	7
Details	HISTONE_H3_1 Histone H3 signature 1. KAPRKQL

Chain	Residue	Details
A	LYS14-LEU20

site_id	PS00357
Number of Residues	23
Details	HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG

Chain	Residue	Details
D	ARG89-GLY111

site_id	PS00518
Number of Residues	10
Details	ZF_RING_1 Zinc finger RING-type signature. ClHsFCktCI

Chain	Residue	Details
M	CYS34-ILE43
N	CYS67-ILE76

site_id	PS00959
Number of Residues	9
Details	HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI

Chain	Residue	Details
A	PRO66-ILE74

site_id	PS01358
Number of Residues	20
Details	ZF_RANBP2_1 Zinc finger RanBP2-type signature. WdCsv..CtfrNsaeafkCsiC

Chain	Residue	Details
L	TRP25-CYS44

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI2
Number of Residues	4
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Modified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine; by PAK2","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
Details	Modified residue: {"description":"N6-methacryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	79
Details	Zinc finger: {"description":"RING-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00175","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	14
Details	Motif: {"description":"Nuclear localization signal","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	5
Details	Region: {"description":"Interaction with nucleosomes via an acidic patch on histone H2A and histone H2B","evidences":[{"source":"PubMed","id":"25355358","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"25519132","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"Q9CQJ4","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)