3DQV

Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006508	biological_process	proteolysis
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0009653	biological_process	anatomical structure morphogenesis
A	0016567	biological_process	protein ubiquitination
A	0019941	biological_process	modification-dependent protein catabolic process
A	0030162	biological_process	regulation of proteolysis
A	0031386	molecular_function	protein tag activity
A	0031625	molecular_function	ubiquitin protein ligase binding
A	0036211	biological_process	protein modification process
A	0045116	biological_process	protein neddylation
A	0070062	cellular_component	extracellular exosome
A	0072757	biological_process	cellular response to camptothecin
A	0098794	cellular_component	postsynapse
A	0098978	cellular_component	glutamatergic synapse
A	0150052	biological_process	regulation of postsynapse assembly
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	0006508	biological_process	proteolysis
B	0006511	biological_process	ubiquitin-dependent protein catabolic process
B	0009653	biological_process	anatomical structure morphogenesis
B	0016567	biological_process	protein ubiquitination
B	0019941	biological_process	modification-dependent protein catabolic process
B	0030162	biological_process	regulation of proteolysis
B	0031386	molecular_function	protein tag activity
B	0031625	molecular_function	ubiquitin protein ligase binding
B	0036211	biological_process	protein modification process
B	0045116	biological_process	protein neddylation
B	0070062	cellular_component	extracellular exosome
B	0072757	biological_process	cellular response to camptothecin
B	0098794	cellular_component	postsynapse
B	0098978	cellular_component	glutamatergic synapse
B	0150052	biological_process	regulation of postsynapse assembly
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	0006511	biological_process	ubiquitin-dependent protein catabolic process
D	0031461	cellular_component	cullin-RING ubiquitin ligase complex
D	0031625	molecular_function	ubiquitin protein ligase binding
R	0000082	biological_process	G1/S transition of mitotic cell cycle
R	0000122	biological_process	negative regulation of transcription by RNA polymerase II
R	0000165	biological_process	MAPK cascade
R	0000209	biological_process	protein polyubiquitination
R	0004842	molecular_function	ubiquitin-protein transferase activity
R	0005515	molecular_function	protein binding
R	0005634	cellular_component	nucleus
R	0005654	cellular_component	nucleoplasm
R	0005737	cellular_component	cytoplasm
R	0005794	cellular_component	Golgi apparatus
R	0005813	cellular_component	centrosome
R	0005829	cellular_component	cytosol
R	0006281	biological_process	DNA repair
R	0006283	biological_process	transcription-coupled nucleotide-excision repair
R	0006289	biological_process	nucleotide-excision repair
R	0006355	biological_process	regulation of DNA-templated transcription
R	0006511	biological_process	ubiquitin-dependent protein catabolic process
R	0006513	biological_process	protein monoubiquitination
R	0006879	biological_process	intracellular iron ion homeostasis
R	0006974	biological_process	DNA damage response
R	0007283	biological_process	spermatogenesis
R	0007346	biological_process	regulation of mitotic cell cycle
R	0008270	molecular_function	zinc ion binding
R	0008283	biological_process	cell population proliferation
R	0010506	biological_process	regulation of autophagy
R	0010564	biological_process	regulation of cell cycle process
R	0010824	biological_process	regulation of centrosome duplication
R	0014033	biological_process	neural crest cell differentiation
R	0016567	biological_process	protein ubiquitination
R	0016740	molecular_function	transferase activity
R	0019005	cellular_component	SCF ubiquitin ligase complex
R	0019788	molecular_function	NEDD8 transferase activity
R	0030174	biological_process	regulation of DNA-templated DNA replication initiation
R	0030510	biological_process	regulation of BMP signaling pathway
R	0030891	cellular_component	VCB complex
R	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
R	0031297	biological_process	replication fork processing
R	0031461	cellular_component	cullin-RING ubiquitin ligase complex
R	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
R	0031463	cellular_component	Cul3-RING ubiquitin ligase complex
R	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
R	0031465	cellular_component	Cul4B-RING E3 ubiquitin ligase complex
R	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
R	0031467	cellular_component	Cul7-RING ubiquitin ligase complex
R	0031625	molecular_function	ubiquitin protein ligase binding
R	0032006	biological_process	regulation of TOR signaling
R	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
R	0032480	biological_process	negative regulation of type I interferon production
R	0032814	biological_process	regulation of natural killer cell activation
R	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
R	0034599	biological_process	cellular response to oxidative stress
R	0034644	biological_process	cellular response to UV
R	0040029	biological_process	epigenetic regulation of gene expression
R	0042110	biological_process	T cell activation
R	0042127	biological_process	regulation of cell population proliferation
R	0042752	biological_process	regulation of circadian rhythm
R	0042770	biological_process	signal transduction in response to DNA damage
R	0042981	biological_process	regulation of apoptotic process
R	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
R	0043124	biological_process	negative regulation of canonical NF-kappaB signal transduction
R	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
R	0043687	biological_process	post-translational protein modification
R	0044314	biological_process	protein K27-linked ubiquitination
R	0044877	molecular_function	protein-containing complex binding
R	0045116	biological_process	protein neddylation
R	0045732	biological_process	positive regulation of protein catabolic process
R	0045995	biological_process	regulation of embryonic development
R	0046627	biological_process	negative regulation of insulin receptor signaling pathway
R	0046872	molecular_function	metal ion binding
R	0050727	biological_process	regulation of inflammatory response
R	0051298	biological_process	centrosome duplication
R	0051726	biological_process	regulation of cell cycle
R	0060090	molecular_function	molecular adaptor activity
R	0060173	biological_process	limb development
R	0060271	biological_process	cilium assembly
R	0060964	biological_process	regulation of miRNA-mediated gene silencing
R	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
R	0061630	molecular_function	ubiquitin protein ligase activity
R	0061663	molecular_function	NEDD8 ligase activity
R	0062197	biological_process	cellular response to chemical stress
R	0070936	biological_process	protein K48-linked ubiquitination
R	0071230	biological_process	cellular response to amino acid stimulus
R	0080008	cellular_component	Cul4-RING E3 ubiquitin ligase complex
R	0080135	biological_process	regulation of cellular response to stress
R	0090090	biological_process	negative regulation of canonical Wnt signaling pathway
R	0090734	cellular_component	site of DNA damage
R	0097602	molecular_function	cullin family protein binding
R	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
R	0160240	biological_process	RNA polymerase II transcription initiation surveillance
R	0160276	biological_process	negative regulation of beige fat cell differentiation
R	1900076	biological_process	regulation of cellular response to insulin stimulus
R	1901524	biological_process	regulation of mitophagy
R	1901525	biological_process	negative regulation of mitophagy
R	1901987	biological_process	regulation of cell cycle phase transition
R	1902412	biological_process	regulation of mitotic cytokinesis
R	1902499	biological_process	positive regulation of protein autoubiquitination
R	1902883	biological_process	negative regulation of response to oxidative stress
R	1904178	biological_process	negative regulation of adipose tissue development
R	1904263	biological_process	positive regulation of TORC1 signaling
R	1904415	biological_process	regulation of xenophagy
R	1990116	biological_process	ribosome-associated ubiquitin-dependent protein catabolic process
R	2000001	biological_process	regulation of DNA damage checkpoint
R	2000036	biological_process	regulation of stem cell population maintenance
R	2000104	biological_process	negative regulation of DNA-templated DNA replication
Y	0000082	biological_process	G1/S transition of mitotic cell cycle
Y	0000122	biological_process	negative regulation of transcription by RNA polymerase II
Y	0000165	biological_process	MAPK cascade
Y	0000209	biological_process	protein polyubiquitination
Y	0004842	molecular_function	ubiquitin-protein transferase activity
Y	0005515	molecular_function	protein binding
Y	0005634	cellular_component	nucleus
Y	0005654	cellular_component	nucleoplasm
Y	0005737	cellular_component	cytoplasm
Y	0005794	cellular_component	Golgi apparatus
Y	0005813	cellular_component	centrosome
Y	0005829	cellular_component	cytosol
Y	0006281	biological_process	DNA repair
Y	0006283	biological_process	transcription-coupled nucleotide-excision repair
Y	0006289	biological_process	nucleotide-excision repair
Y	0006355	biological_process	regulation of DNA-templated transcription
Y	0006511	biological_process	ubiquitin-dependent protein catabolic process
Y	0006513	biological_process	protein monoubiquitination
Y	0006879	biological_process	intracellular iron ion homeostasis
Y	0006974	biological_process	DNA damage response
Y	0007283	biological_process	spermatogenesis
Y	0007346	biological_process	regulation of mitotic cell cycle
Y	0008270	molecular_function	zinc ion binding
Y	0008283	biological_process	cell population proliferation
Y	0010506	biological_process	regulation of autophagy
Y	0010564	biological_process	regulation of cell cycle process
Y	0010824	biological_process	regulation of centrosome duplication
Y	0014033	biological_process	neural crest cell differentiation
Y	0016567	biological_process	protein ubiquitination
Y	0016740	molecular_function	transferase activity
Y	0019005	cellular_component	SCF ubiquitin ligase complex
Y	0019788	molecular_function	NEDD8 transferase activity
Y	0030174	biological_process	regulation of DNA-templated DNA replication initiation
Y	0030510	biological_process	regulation of BMP signaling pathway
Y	0030891	cellular_component	VCB complex
Y	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
Y	0031297	biological_process	replication fork processing
Y	0031461	cellular_component	cullin-RING ubiquitin ligase complex
Y	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
Y	0031463	cellular_component	Cul3-RING ubiquitin ligase complex
Y	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
Y	0031465	cellular_component	Cul4B-RING E3 ubiquitin ligase complex
Y	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
Y	0031467	cellular_component	Cul7-RING ubiquitin ligase complex
Y	0031625	molecular_function	ubiquitin protein ligase binding
Y	0032006	biological_process	regulation of TOR signaling
Y	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
Y	0032480	biological_process	negative regulation of type I interferon production
Y	0032814	biological_process	regulation of natural killer cell activation
Y	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
Y	0034599	biological_process	cellular response to oxidative stress
Y	0034644	biological_process	cellular response to UV
Y	0040029	biological_process	epigenetic regulation of gene expression
Y	0042110	biological_process	T cell activation
Y	0042127	biological_process	regulation of cell population proliferation
Y	0042752	biological_process	regulation of circadian rhythm
Y	0042770	biological_process	signal transduction in response to DNA damage
Y	0042981	biological_process	regulation of apoptotic process
Y	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
Y	0043124	biological_process	negative regulation of canonical NF-kappaB signal transduction
Y	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
Y	0043687	biological_process	post-translational protein modification
Y	0044314	biological_process	protein K27-linked ubiquitination
Y	0044877	molecular_function	protein-containing complex binding
Y	0045116	biological_process	protein neddylation
Y	0045732	biological_process	positive regulation of protein catabolic process
Y	0045995	biological_process	regulation of embryonic development
Y	0046627	biological_process	negative regulation of insulin receptor signaling pathway
Y	0046872	molecular_function	metal ion binding
Y	0050727	biological_process	regulation of inflammatory response
Y	0051298	biological_process	centrosome duplication
Y	0051726	biological_process	regulation of cell cycle
Y	0060090	molecular_function	molecular adaptor activity
Y	0060173	biological_process	limb development
Y	0060271	biological_process	cilium assembly
Y	0060964	biological_process	regulation of miRNA-mediated gene silencing
Y	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
Y	0061630	molecular_function	ubiquitin protein ligase activity
Y	0061663	molecular_function	NEDD8 ligase activity
Y	0062197	biological_process	cellular response to chemical stress
Y	0070936	biological_process	protein K48-linked ubiquitination
Y	0071230	biological_process	cellular response to amino acid stimulus
Y	0080008	cellular_component	Cul4-RING E3 ubiquitin ligase complex
Y	0080135	biological_process	regulation of cellular response to stress
Y	0090090	biological_process	negative regulation of canonical Wnt signaling pathway
Y	0090734	cellular_component	site of DNA damage
Y	0097602	molecular_function	cullin family protein binding
Y	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
Y	0160240	biological_process	RNA polymerase II transcription initiation surveillance
Y	0160276	biological_process	negative regulation of beige fat cell differentiation
Y	1900076	biological_process	regulation of cellular response to insulin stimulus
Y	1901524	biological_process	regulation of mitophagy
Y	1901525	biological_process	negative regulation of mitophagy
Y	1901987	biological_process	regulation of cell cycle phase transition
Y	1902412	biological_process	regulation of mitotic cytokinesis
Y	1902499	biological_process	positive regulation of protein autoubiquitination
Y	1902883	biological_process	negative regulation of response to oxidative stress
Y	1904178	biological_process	negative regulation of adipose tissue development
Y	1904263	biological_process	positive regulation of TORC1 signaling
Y	1904415	biological_process	regulation of xenophagy
Y	1990116	biological_process	ribosome-associated ubiquitin-dependent protein catabolic process
Y	2000001	biological_process	regulation of DNA damage checkpoint
Y	2000036	biological_process	regulation of stem cell population maintenance
Y	2000104	biological_process	negative regulation of DNA-templated DNA replication

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN R 4004

Chain	Residue
R	CYS53
R	CYS56
R	CYS68
R	HIS82

---

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN R 4005

Chain	Residue
R	CYS42
R	CYS45
R	HIS80
R	CYS83

---

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN R 4006

Chain	Residue
R	HIS77
R	CYS94
R	ASP97
R	CYS75

---

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN Y 4001

Chain	Residue
Y	CYS75
Y	HIS77
Y	ASP97

---

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN Y 4002

Chain	Residue
Y	CYS42
Y	CYS45
Y	HIS80
Y	CYS83

---

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN Y 4003

Chain	Residue
Y	CYS53
Y	CYS56
Y	CYS68
Y	HIS82

---

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	LYS127-ASP152

---

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

Chain	Residue	Details
C	ILE1753-ALA1780

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Site: {"description":"Interaction with UBE1C","evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	Modified residue: {"description":"(Microbial infection) Deamidated glutamine","evidences":[{"source":"PubMed","id":"20688984","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21903097","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23175788","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23589306","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26632597","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P29595","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in NEDD8)","evidences":[{"source":"PubMed","id":"18805092","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"33268465","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34518685","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"7ONI","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	14
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11961546","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"38605244","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1LDJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1LDK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U6G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HYE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DPL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DQV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3RTR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4F52","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4P5O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8Q7H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8RHZ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11961546","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"38605244","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1LDJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1LDK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U6G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HYE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DPL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DQV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3RTR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4F52","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4P5O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7Z8B","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8Q7H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8RHZ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11961546","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"38605244","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1LDJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1LDK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U6G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HYE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DQV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3RTR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4F52","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4P5O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8Q7H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8RHZ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---