8Q7H

Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused cullin dimer

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0000226	biological_process	microtubule cytoskeleton organization
A	0004842	molecular_function	ubiquitin-protein transferase activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0007088	biological_process	regulation of mitotic nuclear division
A	0008270	molecular_function	zinc ion binding
A	0016567	biological_process	protein ubiquitination
A	0016740	molecular_function	transferase activity
A	0031461	cellular_component	cullin-RING ubiquitin ligase complex
A	0031625	molecular_function	ubiquitin protein ligase binding
A	0046872	molecular_function	metal ion binding
A	0061630	molecular_function	ubiquitin protein ligase activity
B	0000166	molecular_function	nucleotide binding
B	0000226	biological_process	microtubule cytoskeleton organization
B	0004842	molecular_function	ubiquitin-protein transferase activity
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006511	biological_process	ubiquitin-dependent protein catabolic process
B	0007088	biological_process	regulation of mitotic nuclear division
B	0008270	molecular_function	zinc ion binding
B	0016567	biological_process	protein ubiquitination
B	0016740	molecular_function	transferase activity
B	0031461	cellular_component	cullin-RING ubiquitin ligase complex
B	0031625	molecular_function	ubiquitin protein ligase binding
B	0046872	molecular_function	metal ion binding
B	0061630	molecular_function	ubiquitin protein ligase activity
C	0000045	biological_process	autophagosome assembly
C	0000082	biological_process	G1/S transition of mitotic cell cycle
C	0000165	biological_process	MAPK cascade
C	0000209	biological_process	protein polyubiquitination
C	0000423	biological_process	mitophagy
C	0001837	biological_process	epithelial to mesenchymal transition
C	0004842	molecular_function	ubiquitin-protein transferase activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006281	biological_process	DNA repair
C	0006283	biological_process	transcription-coupled nucleotide-excision repair
C	0006366	biological_process	transcription by RNA polymerase II
C	0006368	biological_process	transcription elongation by RNA polymerase II
C	0006511	biological_process	ubiquitin-dependent protein catabolic process
C	0006513	biological_process	protein monoubiquitination
C	0006915	biological_process	apoptotic process
C	0006974	biological_process	DNA damage response
C	0006979	biological_process	response to oxidative stress
C	0007040	biological_process	lysosome organization
C	0007283	biological_process	spermatogenesis
C	0007346	biological_process	regulation of mitotic cell cycle
C	0008270	molecular_function	zinc ion binding
C	0008286	biological_process	insulin receptor signaling pathway
C	0010507	biological_process	negative regulation of autophagy
C	0010508	biological_process	positive regulation of autophagy
C	0016567	biological_process	protein ubiquitination
C	0016740	molecular_function	transferase activity
C	0019005	cellular_component	SCF ubiquitin ligase complex
C	0019221	biological_process	cytokine-mediated signaling pathway
C	0019788	molecular_function	NEDD8 transferase activity
C	0030163	biological_process	protein catabolic process
C	0030330	biological_process	DNA damage response, signal transduction by p53 class mediator
C	0030891	cellular_component	VCB complex
C	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
C	0031461	cellular_component	cullin-RING ubiquitin ligase complex
C	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
C	0031463	cellular_component	Cul3-RING ubiquitin ligase complex
C	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
C	0031465	cellular_component	Cul4B-RING E3 ubiquitin ligase complex
C	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
C	0031467	cellular_component	Cul7-RING ubiquitin ligase complex
C	0031625	molecular_function	ubiquitin protein ligase binding
C	0031669	biological_process	cellular response to nutrient levels
C	0032435	biological_process	negative regulation of proteasomal ubiquitin-dependent protein catabolic process
C	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
C	0032480	biological_process	negative regulation of type I interferon production
C	0032481	biological_process	positive regulation of type I interferon production
C	0032869	biological_process	cellular response to insulin stimulus
C	0034198	biological_process	cellular response to amino acid starvation
C	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
C	0034599	biological_process	cellular response to oxidative stress
C	0034644	biological_process	cellular response to UV
C	0035279	biological_process	miRNA-mediated gene silencing by mRNA destabilization
C	0038066	biological_process	p38MAPK cascade
C	0038202	biological_process	TORC1 signaling
C	0042110	biological_process	T cell activation
C	0042770	biological_process	signal transduction in response to DNA damage
C	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
C	0043124	biological_process	negative regulation of canonical NF-kappaB signal transduction
C	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
C	0043687	biological_process	post-translational protein modification
C	0044877	molecular_function	protein-containing complex binding
C	0045116	biological_process	protein neddylation
C	0045727	biological_process	positive regulation of translation
C	0045732	biological_process	positive regulation of protein catabolic process
C	0045944	biological_process	positive regulation of transcription by RNA polymerase II
C	0046627	biological_process	negative regulation of insulin receptor signaling pathway
C	0046872	molecular_function	metal ion binding
C	0060090	molecular_function	molecular adaptor activity
C	0060337	biological_process	type I interferon-mediated signaling pathway
C	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
C	0061630	molecular_function	ubiquitin protein ligase activity
C	0061663	molecular_function	NEDD8 ligase activity
C	0062197	biological_process	cellular response to chemical stress
C	0070294	biological_process	renal sodium ion absorption
C	0070936	biological_process	protein K48-linked ubiquitination
C	0071230	biological_process	cellular response to amino acid stimulus
C	0080008	cellular_component	Cul4-RING E3 ubiquitin ligase complex
C	0090090	biological_process	negative regulation of canonical Wnt signaling pathway
C	0090734	cellular_component	site of DNA damage
C	0097510	biological_process	base-excision repair, AP site formation via deaminated base removal
C	0097602	molecular_function	cullin family protein binding
C	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
C	0160240	biological_process	RNA polymerase II transcription initiation surveillance
C	1900076	biological_process	regulation of cellular response to insulin stimulus
C	1901525	biological_process	negative regulation of mitophagy
C	1901797	biological_process	negative regulation of signal transduction by p53 class mediator
C	1902499	biological_process	positive regulation of protein autoubiquitination
C	1902883	biological_process	negative regulation of response to oxidative stress
C	1904037	biological_process	positive regulation of epithelial cell apoptotic process
C	1904262	biological_process	negative regulation of TORC1 signaling
C	1904263	biological_process	positive regulation of TORC1 signaling
C	2000059	biological_process	negative regulation of ubiquitin-dependent protein catabolic process
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
N	0005515	molecular_function	protein binding
N	0005634	cellular_component	nucleus
N	0005654	cellular_component	nucleoplasm
N	0005737	cellular_component	cytoplasm
N	0005829	cellular_component	cytosol
N	0006357	biological_process	regulation of transcription by RNA polymerase II
N	0006508	biological_process	proteolysis
N	0006511	biological_process	ubiquitin-dependent protein catabolic process
N	0008104	biological_process	protein localization
N	0009653	biological_process	anatomical structure morphogenesis
N	0016567	biological_process	protein ubiquitination
N	0019941	biological_process	modification-dependent protein catabolic process
N	0030162	biological_process	regulation of proteolysis
N	0031386	molecular_function	protein tag activity
N	0031625	molecular_function	ubiquitin protein ligase binding
N	0036211	biological_process	protein modification process
N	0045116	biological_process	protein neddylation
N	0070062	cellular_component	extracellular exosome
N	0072757	biological_process	cellular response to camptothecin
N	0098794	cellular_component	postsynapse
N	0098978	cellular_component	glutamatergic synapse
N	0150052	biological_process	regulation of postsynapse assembly

Functional Information from PROSITE/UniProt

site_id	PS00086
Number of Residues	10
Details	CYTOCHROME_P450 Cytochrome P450 cysteine heme-iron ligand signature. FGgDSTSCIG

Chain	Residue	Details
A	PHE1237-GLY1246

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

Chain	Residue	Details
N	LYS27-ASP52

---

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

Chain	Residue	Details
A	CYS2257-LEU2266

---

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

Chain	Residue	Details
A	VAL1926-ALA1953

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	SITE: Interaction with UBE1C => ECO:0000269|PubMed:14690597

Chain	Residue	Details
N	LEU8
N	ILE44

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site_id	SWS_FT_FI2
Number of Residues	1
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
N	GLN40
D	CYS75
D	HIS77
D	HIS80
D	CYS94
D	ASP97
C	CYS45
C	CYS75
C	HIS77
C	HIS80
C	CYS94
C	ASP97
D	CYS42
D	CYS45

---

site_id	SWS_FT_FI3
Number of Residues	1
Details	MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P29595

Chain	Residue	Details
N	LYS48
C	CYS56
C	CYS68
C	HIS82
D	CYS53
D	CYS56
D	CYS68
D	HIS82

---

site_id	SWS_FT_FI4
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) => ECO:0000269|PubMed:38316879

Chain	Residue	Details
N	GLY76
D	CYS83

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	MOD_RES: N-acetylmethionine => ECO:0007744|PubMed:20068231

Chain	Residue	Details
C	MET1
D	MET1

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	MOD_RES: N-acetylalanine; in E3 ubiquitin-protein ligase RBX1, N-terminally processed => ECO:0000269|Ref.8, ECO:0007744|PubMed:19413330, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:22223895, ECO:0007744|PubMed:22814378

Chain	Residue	Details
C	ALA2
A	CYS2166
A	CYS2181
A	CYS2184
A	CYS2189
A	CYS2192
A	HIS2198
A	CYS2203
B	CYS2070
B	CYS2073
B	CYS2088
D	ALA2
B	HIS2090
B	CYS2093
B	CYS2096
B	CYS2115
B	CYS2120
B	CYS2160
B	CYS2166
B	CYS2181
B	CYS2184
B	CYS2189
A	CYS2088
B	CYS2192
B	HIS2198
B	CYS2203
A	HIS2090
A	CYS2093
A	CYS2096
A	CYS2115
A	CYS2120
A	CYS2160

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163

Chain	Residue	Details
C	THR9
B	CYS2239
B	CYS2254
B	CYS2257
B	CYS2262
B	CYS2265
B	HIS2273
B	CYS2279
D	THR9
A	CYS2254
A	CYS2257
A	CYS2262
A	CYS2265
A	HIS2273
A	CYS2279
B	CYS2236

---

site_id	SWS_FT_FI8
Number of Residues	6
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163

Chain	Residue	Details
A	SER976
A	SER1457
A	SER2436
B	SER976
B	SER1457
B	SER2436

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:38605244

Chain	Residue	Details
A	LYS87
B	LYS87

---

site_id	SWS_FT_FI10
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in NEDD8) => ECO:0000269|PubMed:38605244, ECO:0007744|PDB:8Q7H

Chain	Residue	Details
A	LYS1881
B	LYS1881

---