Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

7JZV

Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000122	biological_process	negative regulation of transcription by RNA polymerase II
A	0000166	molecular_function	nucleotide binding
A	0000209	biological_process	protein polyubiquitination
A	0004842	molecular_function	ubiquitin-protein transferase activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005829	cellular_component	cytosol
A	0005886	cellular_component	plasma membrane
A	0006281	biological_process	DNA repair
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0006513	biological_process	protein monoubiquitination
A	0006915	biological_process	apoptotic process
A	0006974	biological_process	DNA damage response
A	0010008	cellular_component	endosome membrane
A	0016567	biological_process	protein ubiquitination
A	0016740	molecular_function	transferase activity
A	0030514	biological_process	negative regulation of BMP signaling pathway
A	0036211	biological_process	protein modification process
A	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
A	0046872	molecular_function	metal ion binding
A	0051865	biological_process	protein autoubiquitination
A	0061630	molecular_function	ubiquitin protein ligase activity
A	0061631	molecular_function	ubiquitin conjugating enzyme activity
A	0070062	cellular_component	extracellular exosome
A	0070936	biological_process	protein K48-linked ubiquitination
A	0070979	biological_process	protein K11-linked ubiquitination
A	0085020	biological_process	protein K6-linked ubiquitination
A	1903955	biological_process	obsolete positive regulation of protein targeting to mitochondrion
B	0003697	molecular_function	single-stranded DNA binding
B	0006301	biological_process	DNA damage tolerance
B	0006513	biological_process	protein monoubiquitination
B	0061630	molecular_function	ubiquitin protein ligase activity
n	0000786	cellular_component	nucleosome
n	0003677	molecular_function	DNA binding
n	0005515	molecular_function	protein binding
n	0005634	cellular_component	nucleus
n	0005654	cellular_component	nucleoplasm
n	0005694	cellular_component	chromosome
n	0030527	molecular_function	structural constituent of chromatin
n	0031507	biological_process	heterochromatin formation
n	0046982	molecular_function	protein heterodimerization activity
n	0070062	cellular_component	extracellular exosome
N	0000786	cellular_component	nucleosome
N	0003677	molecular_function	DNA binding
N	0005515	molecular_function	protein binding
N	0005634	cellular_component	nucleus
N	0005654	cellular_component	nucleoplasm
N	0005694	cellular_component	chromosome
N	0030527	molecular_function	structural constituent of chromatin
N	0031507	biological_process	heterochromatin formation
N	0046982	molecular_function	protein heterodimerization activity
N	0070062	cellular_component	extracellular exosome
o	0000786	cellular_component	nucleosome
o	0002227	biological_process	innate immune response in mucosa
o	0003677	molecular_function	DNA binding
o	0005515	molecular_function	protein binding
o	0005615	cellular_component	extracellular space
o	0005634	cellular_component	nucleus
o	0005654	cellular_component	nucleoplasm
o	0005694	cellular_component	chromosome
o	0006325	biological_process	chromatin organization
o	0019731	biological_process	antibacterial humoral response
o	0030527	molecular_function	structural constituent of chromatin
o	0031640	biological_process	killing of cells of another organism
o	0042742	biological_process	defense response to bacterium
o	0046982	molecular_function	protein heterodimerization activity
o	0050829	biological_process	defense response to Gram-negative bacterium
o	0050830	biological_process	defense response to Gram-positive bacterium
o	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
O	0000786	cellular_component	nucleosome
O	0002227	biological_process	innate immune response in mucosa
O	0003677	molecular_function	DNA binding
O	0005515	molecular_function	protein binding
O	0005615	cellular_component	extracellular space
O	0005634	cellular_component	nucleus
O	0005654	cellular_component	nucleoplasm
O	0005694	cellular_component	chromosome
O	0006325	biological_process	chromatin organization
O	0019731	biological_process	antibacterial humoral response
O	0030527	molecular_function	structural constituent of chromatin
O	0031640	biological_process	killing of cells of another organism
O	0042742	biological_process	defense response to bacterium
O	0046982	molecular_function	protein heterodimerization activity
O	0050829	biological_process	defense response to Gram-negative bacterium
O	0050830	biological_process	defense response to Gram-positive bacterium
O	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
p	0000786	cellular_component	nucleosome
p	0003677	molecular_function	DNA binding
p	0005515	molecular_function	protein binding
p	0005576	cellular_component	extracellular region
p	0005634	cellular_component	nucleus
p	0005654	cellular_component	nucleoplasm
p	0005694	cellular_component	chromosome
p	0006325	biological_process	chromatin organization
p	0006334	biological_process	nucleosome assembly
p	0030527	molecular_function	structural constituent of chromatin
p	0031492	molecular_function	nucleosomal DNA binding
p	0031507	biological_process	heterochromatin formation
p	0046982	molecular_function	protein heterodimerization activity
p	0070062	cellular_component	extracellular exosome
P	0000786	cellular_component	nucleosome
P	0003677	molecular_function	DNA binding
P	0005515	molecular_function	protein binding
P	0005576	cellular_component	extracellular region
P	0005634	cellular_component	nucleus
P	0005654	cellular_component	nucleoplasm
P	0005694	cellular_component	chromosome
P	0006325	biological_process	chromatin organization
P	0006334	biological_process	nucleosome assembly
P	0030527	molecular_function	structural constituent of chromatin
P	0031492	molecular_function	nucleosomal DNA binding
P	0031507	biological_process	heterochromatin formation
P	0046982	molecular_function	protein heterodimerization activity
P	0070062	cellular_component	extracellular exosome
q	0000781	cellular_component	chromosome, telomeric region
q	0000786	cellular_component	nucleosome
q	0003677	molecular_function	DNA binding
q	0003723	molecular_function	RNA binding
q	0005515	molecular_function	protein binding
q	0005576	cellular_component	extracellular region
q	0005634	cellular_component	nucleus
q	0005654	cellular_component	nucleoplasm
q	0005694	cellular_component	chromosome
q	0006325	biological_process	chromatin organization
q	0006334	biological_process	nucleosome assembly
q	0016020	cellular_component	membrane
q	0030527	molecular_function	structural constituent of chromatin
q	0032200	biological_process	telomere organization
q	0032991	cellular_component	protein-containing complex
q	0045653	biological_process	negative regulation of megakaryocyte differentiation
q	0046982	molecular_function	protein heterodimerization activity
q	0061644	biological_process	protein localization to CENP-A containing chromatin
q	0070062	cellular_component	extracellular exosome
Q	0000781	cellular_component	chromosome, telomeric region
Q	0000786	cellular_component	nucleosome
Q	0003677	molecular_function	DNA binding
Q	0003723	molecular_function	RNA binding
Q	0005515	molecular_function	protein binding
Q	0005576	cellular_component	extracellular region
Q	0005634	cellular_component	nucleus
Q	0005654	cellular_component	nucleoplasm
Q	0005694	cellular_component	chromosome
Q	0006325	biological_process	chromatin organization
Q	0006334	biological_process	nucleosome assembly
Q	0016020	cellular_component	membrane
Q	0030527	molecular_function	structural constituent of chromatin
Q	0032200	biological_process	telomere organization
Q	0032991	cellular_component	protein-containing complex
Q	0045653	biological_process	negative regulation of megakaryocyte differentiation
Q	0046982	molecular_function	protein heterodimerization activity
Q	0061644	biological_process	protein localization to CENP-A containing chromatin
Q	0070062	cellular_component	extracellular exosome

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
N	ALA21-VAL27

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

Chain	Residue	Details
Q	GLY14-HIS18

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

Chain	Residue	Details
P	LYS14-LEU20

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

Chain	Residue	Details
O	ARG92-GLY114

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

Chain	Residue	Details
B	CYS66-VAL75
A	CYS39-MET48

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

Chain	Residue	Details
P	PRO66-ILE74

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI2
Number of Residues	78
Details	Zinc finger: {"description":"RING-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00175","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	1
Details	Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10133","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	93
Details	Region: {"description":"Interaction with BRCA1"}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	2
Details	Modified residue: {"description":"N6-isonicotinyllysine","evidences":[{"source":"PubMed","id":"34545082","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
Details	Modified residue: {"description":"N6-crotonyllysine; alternate","evidences":[{"source":"PubMed","id":"21925322","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	4
Details	Modified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine","evidences":[{"source":"PubMed","id":"24681537","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	16
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	2
Details	Modified residue: {"description":"N6-glutaryllysine","evidences":[{"source":"PubMed","id":"31542297","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	2
Details	Modified residue: {"description":"N5-methylglutamine","evidences":[{"source":"PubMed","id":"24352239","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	4
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"PubMed","id":"31542297","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"22713238","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22980979","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	2
Details	Modified residue: {"description":"PolyADP-ribosyl glutamic acid","evidences":[{"source":"UniProtKB","id":"Q64475","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine; by AMPK","evidences":[{"source":"UniProtKB","id":"Q8CGP1","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	2
Details	Modified residue: {"description":"N6-lactoyllysine; alternate","evidences":[{"source":"PubMed","id":"31645732","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	4
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"16627869","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	2
Details	Modified residue: {"description":"N6-isonicotinyllysine; alternate","evidences":[{"source":"PubMed","id":"34545082","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	2
Details	Modified residue: {"description":"Dimethylated arginine","evidences":[{"source":"UniProtKB","id":"Q96A08","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	4
Details	Modified residue: {"description":"N6-methacryllysine; alternate","evidences":[{"source":"PubMed","id":"34961760","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	4
Details	Modified residue: {"description":"Omega-N-methylarginine","evidences":[{"source":"UniProtKB","id":"Q96A08","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q00729","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
Number of Residues	2
Details	Glycosylation: {"description":"O-linked (GlcNAc) serine","evidences":[{"source":"UniProtKB","id":"P62807","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI23
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"PubMed","id":"21726816","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI24
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"PubMed","id":"16307923","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16627869","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16713563","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI25
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"20850016","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI26
Number of Residues	2
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"16267050","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17194708","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI27
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"29211711","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI28
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"20850016","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI29
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI30
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI31
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27436229","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI32
Number of Residues	2
Details	Lipidation: {"description":"S-palmitoyl cysteine","evidences":[{"source":"PubMed","id":"21076176","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI33
Number of Residues	4
Details	DNA binding: {}

Chain

Residue

Details

site_id	SWS_FT_FI34
Number of Residues	3
Details	Modified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"PubMed","id":"17267393","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI35
Number of Residues	1
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"12086618","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15964846","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17967882","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20622854","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27338793","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32209475","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI36
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine; by PAK2","evidences":[{"source":"PubMed","id":"21724829","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17081983","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"21406692","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI37
Number of Residues	2
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"15592455","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI38
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62806","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI39
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P62806","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI40
Number of Residues	2
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI41
Number of Residues	5
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI42
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"PubMed","id":"19818714","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI43
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate","evidences":[{"source":"PubMed","id":"30886146","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

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