Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4P5O

Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0031461	cellular_component	cullin-RING ubiquitin ligase complex
A	0031625	molecular_function	ubiquitin protein ligase binding
B	0000165	biological_process	MAPK cascade
B	0000209	biological_process	protein polyubiquitination
B	0004842	molecular_function	ubiquitin-protein transferase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006281	biological_process	DNA repair
B	0006511	biological_process	ubiquitin-dependent protein catabolic process
B	0006513	biological_process	protein monoubiquitination
B	0006974	biological_process	DNA damage response
B	0007283	biological_process	spermatogenesis
B	0008270	molecular_function	zinc ion binding
B	0016567	biological_process	protein ubiquitination
B	0016740	molecular_function	transferase activity
B	0019005	cellular_component	SCF ubiquitin ligase complex
B	0019788	molecular_function	NEDD8 transferase activity
B	0030163	biological_process	protein catabolic process
B	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
B	0031461	cellular_component	cullin-RING ubiquitin ligase complex
B	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
B	0031463	cellular_component	Cul3-RING ubiquitin ligase complex
B	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
B	0031465	cellular_component	Cul4B-RING E3 ubiquitin ligase complex
B	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
B	0031467	cellular_component	Cul7-RING ubiquitin ligase complex
B	0031625	molecular_function	ubiquitin protein ligase binding
B	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
B	0032480	biological_process	negative regulation of type I interferon production
B	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
B	0034644	biological_process	cellular response to UV
B	0042110	biological_process	T cell activation
B	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
B	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
B	0043687	biological_process	post-translational protein modification
B	0045116	biological_process	protein neddylation
B	0045732	biological_process	positive regulation of protein catabolic process
B	0046872	molecular_function	metal ion binding
B	0060090	molecular_function	molecular adaptor activity
B	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
B	0061630	molecular_function	ubiquitin protein ligase activity
B	0061663	molecular_function	NEDD8 ligase activity
B	0062197	biological_process	cellular response to chemical stress
B	0070936	biological_process	protein K48-linked ubiquitination
B	0071230	biological_process	cellular response to amino acid stimulus
B	0090090	biological_process	negative regulation of canonical Wnt signaling pathway
B	0097602	molecular_function	cullin family protein binding
B	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
B	1900076	biological_process	regulation of cellular response to insulin stimulus
B	1902499	biological_process	positive regulation of protein autoubiquitination
B	1902883	biological_process	negative regulation of response to oxidative stress
B	1904263	biological_process	positive regulation of TORC1 signaling
C	0006511	biological_process	ubiquitin-dependent protein catabolic process
C	0031461	cellular_component	cullin-RING ubiquitin ligase complex
C	0031625	molecular_function	ubiquitin protein ligase binding
D	0000165	biological_process	MAPK cascade
D	0000209	biological_process	protein polyubiquitination
D	0004842	molecular_function	ubiquitin-protein transferase activity
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006281	biological_process	DNA repair
D	0006511	biological_process	ubiquitin-dependent protein catabolic process
D	0006513	biological_process	protein monoubiquitination
D	0006974	biological_process	DNA damage response
D	0007283	biological_process	spermatogenesis
D	0008270	molecular_function	zinc ion binding
D	0016567	biological_process	protein ubiquitination
D	0016740	molecular_function	transferase activity
D	0019005	cellular_component	SCF ubiquitin ligase complex
D	0019788	molecular_function	NEDD8 transferase activity
D	0030163	biological_process	protein catabolic process
D	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
D	0031461	cellular_component	cullin-RING ubiquitin ligase complex
D	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
D	0031463	cellular_component	Cul3-RING ubiquitin ligase complex
D	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
D	0031465	cellular_component	Cul4B-RING E3 ubiquitin ligase complex
D	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
D	0031467	cellular_component	Cul7-RING ubiquitin ligase complex
D	0031625	molecular_function	ubiquitin protein ligase binding
D	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
D	0032480	biological_process	negative regulation of type I interferon production
D	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
D	0034644	biological_process	cellular response to UV
D	0042110	biological_process	T cell activation
D	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
D	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
D	0043687	biological_process	post-translational protein modification
D	0045116	biological_process	protein neddylation
D	0045732	biological_process	positive regulation of protein catabolic process
D	0046872	molecular_function	metal ion binding
D	0060090	molecular_function	molecular adaptor activity
D	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
D	0061630	molecular_function	ubiquitin protein ligase activity
D	0061663	molecular_function	NEDD8 ligase activity
D	0062197	biological_process	cellular response to chemical stress
D	0070936	biological_process	protein K48-linked ubiquitination
D	0071230	biological_process	cellular response to amino acid stimulus
D	0090090	biological_process	negative regulation of canonical Wnt signaling pathway
D	0097602	molecular_function	cullin family protein binding
D	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
D	1900076	biological_process	regulation of cellular response to insulin stimulus
D	1902499	biological_process	positive regulation of protein autoubiquitination
D	1902883	biological_process	negative regulation of response to oxidative stress
D	1904263	biological_process	positive regulation of TORC1 signaling
G	0004842	molecular_function	ubiquitin-protein transferase activity
G	0005515	molecular_function	protein binding
G	0005524	molecular_function	ATP binding
G	0005634	cellular_component	nucleus
G	0005654	cellular_component	nucleoplasm
G	0005829	cellular_component	cytosol
G	0016740	molecular_function	transferase activity
G	0019787	molecular_function	ubiquitin-like protein transferase activity
G	0019788	molecular_function	NEDD8 transferase activity
G	0032446	biological_process	protein modification by small protein conjugation
G	0036211	biological_process	protein modification process
G	0043525	biological_process	positive regulation of neuron apoptotic process
G	0043687	biological_process	post-translational protein modification
G	0045116	biological_process	protein neddylation
G	0061654	molecular_function	NEDD8 conjugating enzyme activity
G	0098793	cellular_component	presynapse
G	0098794	cellular_component	postsynapse
G	0098978	cellular_component	glutamatergic synapse
G	0150052	biological_process	regulation of postsynapse assembly
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0005829	cellular_component	cytosol
H	0006357	biological_process	regulation of transcription by RNA polymerase II
H	0006508	biological_process	proteolysis
H	0006511	biological_process	ubiquitin-dependent protein catabolic process
H	0008104	biological_process	protein localization
H	0009653	biological_process	anatomical structure morphogenesis
H	0016567	biological_process	protein ubiquitination
H	0019941	biological_process	modification-dependent protein catabolic process
H	0030162	biological_process	regulation of proteolysis
H	0031386	molecular_function	protein tag activity
H	0031625	molecular_function	ubiquitin protein ligase binding
H	0036211	biological_process	protein modification process
H	0045116	biological_process	protein neddylation
H	0070062	cellular_component	extracellular exosome
H	0098978	cellular_component	glutamatergic synapse
H	0150052	biological_process	regulation of postsynapse assembly
I	0004842	molecular_function	ubiquitin-protein transferase activity
I	0005515	molecular_function	protein binding
I	0005524	molecular_function	ATP binding
I	0005634	cellular_component	nucleus
I	0005654	cellular_component	nucleoplasm
I	0005829	cellular_component	cytosol
I	0016740	molecular_function	transferase activity
I	0019787	molecular_function	ubiquitin-like protein transferase activity
I	0019788	molecular_function	NEDD8 transferase activity
I	0032446	biological_process	protein modification by small protein conjugation
I	0036211	biological_process	protein modification process
I	0043525	biological_process	positive regulation of neuron apoptotic process
I	0043687	biological_process	post-translational protein modification
I	0045116	biological_process	protein neddylation
I	0061654	molecular_function	NEDD8 conjugating enzyme activity
I	0098793	cellular_component	presynapse
I	0098794	cellular_component	postsynapse
I	0098978	cellular_component	glutamatergic synapse
I	0150052	biological_process	regulation of postsynapse assembly
K	0005515	molecular_function	protein binding
K	0005634	cellular_component	nucleus
K	0005654	cellular_component	nucleoplasm
K	0005829	cellular_component	cytosol
K	0006357	biological_process	regulation of transcription by RNA polymerase II
K	0006508	biological_process	proteolysis
K	0006511	biological_process	ubiquitin-dependent protein catabolic process
K	0008104	biological_process	protein localization
K	0009653	biological_process	anatomical structure morphogenesis
K	0016567	biological_process	protein ubiquitination
K	0019941	biological_process	modification-dependent protein catabolic process
K	0030162	biological_process	regulation of proteolysis
K	0031386	molecular_function	protein tag activity
K	0031625	molecular_function	ubiquitin protein ligase binding
K	0036211	biological_process	protein modification process
K	0045116	biological_process	protein neddylation
K	0070062	cellular_component	extracellular exosome
K	0098978	cellular_component	glutamatergic synapse
K	0150052	biological_process	regulation of postsynapse assembly

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue ZN B 201

Chain	Residue
B	CYS42
B	CYS45
B	HIS80
B	CYS83

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN B 202

Chain	Residue
B	CYS75
B	HIS77
B	CYS94
B	ASP97

site_id	AC3
Number of Residues	4
Details	binding site for residue ZN B 203

Chain	Residue
B	CYS56
B	CYS68
B	HIS82
B	CYS53

site_id	AC4
Number of Residues	4
Details	binding site for residue ZN D 201

Chain	Residue
D	CYS42
D	CYS45
D	HIS80
D	CYS83

site_id	AC5
Number of Residues	4
Details	binding site for residue ZN D 202

Chain	Residue
D	CYS75
D	HIS77
D	CYS94
D	ASP97

site_id	AC6
Number of Residues	4
Details	binding site for residue ZN D 203

Chain	Residue
D	CYS53
D	CYS56
D	CYS68
D	HIS82

site_id	AC7
Number of Residues	11
Details	binding site for Di-peptide AME G 1 and ILE G 2

Chain	Residue
F	PRO97
F	SER99
F	VAL102
F	LEU103
F	GLN114
F	CYS115
F	PHE164
F	TYR181
G	LYS3
G	LEU4
G	PHE5

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
K	LYS27-ASP52

site_id	PS01256
Number of Residues	28
Details	CULLIN_1 Cullin family signature. IKkcIdiLIEKeYLeRvdgekdtYsYlA

Chain	Residue	Details
A	ILE749-ALA776

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	SITE: Interaction with UBE1C => ECO:0000269\|PubMed:14690597

Chain	Residue	Details
K	LEU8
K	ILE44
H	LEU8
H	ILE44

site_id	SWS_FT_FI2
Number of Residues	2
Details	MOD_RES: (Microbial infection) Deamidated glutamine => ECO:0000269\|PubMed:20688984, ECO:0000269\|PubMed:21903097, ECO:0000269\|PubMed:23175788, ECO:0000269\|PubMed:23589306, ECO:0000269\|PubMed:26632597

Chain	Residue	Details
K	GLN40
B	CYS94
B	ASP97
D	CYS42
D	CYS45
D	CYS53
D	CYS56
D	CYS68
D	CYS75
D	HIS77
D	HIS80
H	GLN40
D	HIS82
D	CYS94
D	ASP97
B	CYS53
B	CYS56
B	CYS68
B	CYS75
B	HIS77
B	HIS80
B	HIS82

site_id	SWS_FT_FI3
Number of Residues	2
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:P29595

Chain	Residue	Details
K	LYS48
H	LYS48

site_id	SWS_FT_FI4
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Chain	Residue	Details
K	GLY76
G	ARG169
H	GLY76

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)