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	0000045	biological_process	autophagosome assembly
B	0000082	biological_process	G1/S transition of mitotic cell cycle
B	0000165	biological_process	MAPK cascade
B	0000209	biological_process	protein polyubiquitination
B	0000423	biological_process	mitophagy
B	0001837	biological_process	epithelial to mesenchymal transition
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	0006283	biological_process	transcription-coupled nucleotide-excision repair
B	0006366	biological_process	transcription by RNA polymerase II
B	0006368	biological_process	transcription elongation by RNA polymerase II
B	0006511	biological_process	ubiquitin-dependent protein catabolic process
B	0006513	biological_process	protein monoubiquitination
B	0006915	biological_process	apoptotic process
B	0006974	biological_process	DNA damage response
B	0006979	biological_process	response to oxidative stress
B	0007040	biological_process	lysosome organization
B	0007283	biological_process	spermatogenesis
B	0007346	biological_process	regulation of mitotic cell cycle
B	0008270	molecular_function	zinc ion binding
B	0008286	biological_process	insulin receptor signaling pathway
B	0010507	biological_process	negative regulation of autophagy
B	0010508	biological_process	positive regulation of autophagy
B	0016567	biological_process	protein ubiquitination
B	0016740	molecular_function	transferase activity
B	0019005	cellular_component	SCF ubiquitin ligase complex
B	0019221	biological_process	cytokine-mediated signaling pathway
B	0019788	molecular_function	NEDD8 transferase activity
B	0030163	biological_process	protein catabolic process
B	0030330	biological_process	DNA damage response, signal transduction by p53 class mediator
B	0030891	cellular_component	VCB complex
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	0031669	biological_process	cellular response to nutrient levels
B	0032435	biological_process	negative regulation of proteasomal ubiquitin-dependent protein catabolic process
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	0032481	biological_process	positive regulation of type I interferon production
B	0032869	biological_process	cellular response to insulin stimulus
B	0034198	biological_process	cellular response to amino acid starvation
B	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
B	0034599	biological_process	cellular response to oxidative stress
B	0034644	biological_process	cellular response to UV
B	0035279	biological_process	miRNA-mediated gene silencing by mRNA destabilization
B	0038066	biological_process	p38MAPK cascade
B	0038202	biological_process	TORC1 signaling
B	0042110	biological_process	T cell activation
B	0042770	biological_process	signal transduction in response to DNA damage
B	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
B	0043124	biological_process	negative 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	0044877	molecular_function	protein-containing complex binding
B	0045116	biological_process	protein neddylation
B	0045727	biological_process	positive regulation of translation
B	0045732	biological_process	positive regulation of protein catabolic process
B	0045944	biological_process	positive regulation of transcription by RNA polymerase II
B	0046627	biological_process	negative regulation of insulin receptor signaling pathway
B	0046872	molecular_function	metal ion binding
B	0060090	molecular_function	molecular adaptor activity
B	0060337	biological_process	type I interferon-mediated signaling pathway
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	0070294	biological_process	renal sodium ion absorption
B	0070936	biological_process	protein K48-linked ubiquitination
B	0071230	biological_process	cellular response to amino acid stimulus
B	0080008	cellular_component	Cul4-RING E3 ubiquitin ligase complex
B	0090090	biological_process	negative regulation of canonical Wnt signaling pathway
B	0090734	cellular_component	site of DNA damage
B	0097510	biological_process	base-excision repair, AP site formation via deaminated base removal
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	0160240	biological_process	RNA polymerase II transcription initiation surveillance
B	1900076	biological_process	regulation of cellular response to insulin stimulus
B	1901525	biological_process	negative regulation of mitophagy
B	1901797	biological_process	negative regulation of signal transduction by p53 class mediator
B	1902499	biological_process	positive regulation of protein autoubiquitination
B	1902883	biological_process	negative regulation of response to oxidative stress
B	1904037	biological_process	positive regulation of epithelial cell apoptotic process
B	1904262	biological_process	negative regulation of TORC1 signaling
B	1904263	biological_process	positive regulation of TORC1 signaling
B	2000059	biological_process	negative regulation of ubiquitin-dependent protein catabolic process
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	0000045	biological_process	autophagosome assembly
D	0000082	biological_process	G1/S transition of mitotic cell cycle
D	0000165	biological_process	MAPK cascade
D	0000209	biological_process	protein polyubiquitination
D	0000423	biological_process	mitophagy
D	0001837	biological_process	epithelial to mesenchymal transition
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	0006283	biological_process	transcription-coupled nucleotide-excision repair
D	0006366	biological_process	transcription by RNA polymerase II
D	0006368	biological_process	transcription elongation by RNA polymerase II
D	0006511	biological_process	ubiquitin-dependent protein catabolic process
D	0006513	biological_process	protein monoubiquitination
D	0006915	biological_process	apoptotic process
D	0006974	biological_process	DNA damage response
D	0006979	biological_process	response to oxidative stress
D	0007040	biological_process	lysosome organization
D	0007283	biological_process	spermatogenesis
D	0007346	biological_process	regulation of mitotic cell cycle
D	0008270	molecular_function	zinc ion binding
D	0008286	biological_process	insulin receptor signaling pathway
D	0010507	biological_process	negative regulation of autophagy
D	0010508	biological_process	positive regulation of autophagy
D	0016567	biological_process	protein ubiquitination
D	0016740	molecular_function	transferase activity
D	0019005	cellular_component	SCF ubiquitin ligase complex
D	0019221	biological_process	cytokine-mediated signaling pathway
D	0019788	molecular_function	NEDD8 transferase activity
D	0030163	biological_process	protein catabolic process
D	0030330	biological_process	DNA damage response, signal transduction by p53 class mediator
D	0030891	cellular_component	VCB complex
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	0031669	biological_process	cellular response to nutrient levels
D	0032435	biological_process	negative regulation of proteasomal ubiquitin-dependent protein catabolic process
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	0032481	biological_process	positive regulation of type I interferon production
D	0032869	biological_process	cellular response to insulin stimulus
D	0034198	biological_process	cellular response to amino acid starvation
D	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
D	0034599	biological_process	cellular response to oxidative stress
D	0034644	biological_process	cellular response to UV
D	0035279	biological_process	miRNA-mediated gene silencing by mRNA destabilization
D	0038066	biological_process	p38MAPK cascade
D	0038202	biological_process	TORC1 signaling
D	0042110	biological_process	T cell activation
D	0042770	biological_process	signal transduction in response to DNA damage
D	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
D	0043124	biological_process	negative 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	0044877	molecular_function	protein-containing complex binding
D	0045116	biological_process	protein neddylation
D	0045727	biological_process	positive regulation of translation
D	0045732	biological_process	positive regulation of protein catabolic process
D	0045944	biological_process	positive regulation of transcription by RNA polymerase II
D	0046627	biological_process	negative regulation of insulin receptor signaling pathway
D	0046872	molecular_function	metal ion binding
D	0060090	molecular_function	molecular adaptor activity
D	0060337	biological_process	type I interferon-mediated signaling pathway
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	0070294	biological_process	renal sodium ion absorption
D	0070936	biological_process	protein K48-linked ubiquitination
D	0071230	biological_process	cellular response to amino acid stimulus
D	0080008	cellular_component	Cul4-RING E3 ubiquitin ligase complex
D	0090090	biological_process	negative regulation of canonical Wnt signaling pathway
D	0090734	cellular_component	site of DNA damage
D	0097510	biological_process	base-excision repair, AP site formation via deaminated base removal
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	0160240	biological_process	RNA polymerase II transcription initiation surveillance
D	1900076	biological_process	regulation of cellular response to insulin stimulus
D	1901525	biological_process	negative regulation of mitophagy
D	1901797	biological_process	negative regulation of signal transduction by p53 class mediator
D	1902499	biological_process	positive regulation of protein autoubiquitination
D	1902883	biological_process	negative regulation of response to oxidative stress
D	1904037	biological_process	positive regulation of epithelial cell apoptotic process
D	1904262	biological_process	negative regulation of TORC1 signaling
D	1904263	biological_process	positive regulation of TORC1 signaling
D	2000059	biological_process	negative regulation of ubiquitin-dependent protein catabolic process
G	0000166	molecular_function	nucleotide binding
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	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	0005737	cellular_component	cytoplasm
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	0072757	biological_process	cellular response to camptothecin
H	0098794	cellular_component	postsynapse
H	0098978	cellular_component	glutamatergic synapse
H	0150052	biological_process	regulation of postsynapse assembly
I	0000166	molecular_function	nucleotide binding
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	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	0005737	cellular_component	cytoplasm
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	0072757	biological_process	cellular response to camptothecin
K	0098794	cellular_component	postsynapse
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
D	CYS75
D	HIS77
D	HIS80
D	CYS94
D	ASP97
H	GLN40
B	CYS75
B	HIS77
B	HIS80
B	CYS94
B	ASP97
D	CYS42
D	CYS45

---

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
B	CYS68
B	HIS82
D	CYS53
D	CYS56
D	CYS68
D	HIS82

---

site_id	SWS_FT_FI4
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) => ECO:0000269|PubMed:38316879

Chain	Residue	Details
K	GLY76
G	ARG169
H	GLY76

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163

Chain	Residue	Details
B	THR9
D	THR9

---