9KBD

Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO3 SCF ubiquition ligase complex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000082	biological_process	G1/S transition of mitotic cell cycle
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	0005886	cellular_component	plasma membrane
A	0006355	biological_process	regulation of DNA-templated transcription
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0006879	biological_process	intracellular iron ion homeostasis
A	0007346	biological_process	regulation of mitotic cell cycle
A	0010564	biological_process	regulation of cell cycle process
A	0010824	biological_process	regulation of centrosome duplication
A	0014033	biological_process	neural crest cell differentiation
A	0016567	biological_process	protein ubiquitination
A	0019005	cellular_component	SCF ubiquitin ligase complex
A	0030510	biological_process	regulation of BMP signaling pathway
A	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
A	0031461	cellular_component	cullin-RING ubiquitin ligase complex
A	0031625	molecular_function	ubiquitin protein ligase binding
A	0032006	biological_process	regulation of TOR signaling
A	0034599	biological_process	cellular response to oxidative stress
A	0042752	biological_process	regulation of circadian rhythm
A	0042981	biological_process	regulation of apoptotic process
A	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
A	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
A	0050727	biological_process	regulation of inflammatory response
A	0051298	biological_process	centrosome duplication
A	0051726	biological_process	regulation of cell cycle
A	0060173	biological_process	limb development
A	0060271	biological_process	cilium assembly
A	0070936	biological_process	protein K48-linked ubiquitination
A	0097193	biological_process	intrinsic apoptotic signaling pathway
A	0160072	molecular_function	ubiquitin ligase complex scaffold activity
A	1901524	biological_process	regulation of mitophagy
A	1904415	biological_process	regulation of xenophagy
A	1990452	cellular_component	Parkin-FBXW7-Cul1 ubiquitin ligase complex
A	2000001	biological_process	regulation of DNA damage checkpoint
B	0000082	biological_process	G1/S transition of mitotic cell cycle
B	0000209	biological_process	protein polyubiquitination
B	0000785	cellular_component	chromatin
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005737	cellular_component	cytoplasm
B	0005813	cellular_component	centrosome
B	0005829	cellular_component	cytosol
B	0006338	biological_process	chromatin remodeling
B	0006355	biological_process	regulation of DNA-templated transcription
B	0006511	biological_process	ubiquitin-dependent protein catabolic process
B	0006879	biological_process	intracellular iron ion homeostasis
B	0007346	biological_process	regulation of mitotic cell cycle
B	0008013	molecular_function	beta-catenin binding
B	0010564	biological_process	regulation of cell cycle process
B	0010824	biological_process	regulation of centrosome duplication
B	0014033	biological_process	neural crest cell differentiation
B	0016567	biological_process	protein ubiquitination
B	0019005	cellular_component	SCF ubiquitin ligase complex
B	0019904	molecular_function	protein domain specific binding
B	0030510	biological_process	regulation of BMP signaling pathway
B	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
B	0031467	cellular_component	Cul7-RING ubiquitin ligase complex
B	0031507	biological_process	heterochromatin formation
B	0031519	cellular_component	PcG protein complex
B	0032006	biological_process	regulation of TOR signaling
B	0042752	biological_process	regulation of circadian rhythm
B	0042981	biological_process	regulation of apoptotic process
B	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
B	0045892	biological_process	negative regulation of DNA-templated transcription
B	0050727	biological_process	regulation of inflammatory response
B	0051124	biological_process	synaptic assembly at neuromuscular junction
B	0051298	biological_process	centrosome duplication
B	0051457	biological_process	maintenance of protein location in nucleus
B	0051726	biological_process	regulation of cell cycle
B	0060173	biological_process	limb development
B	0060271	biological_process	cilium assembly
B	0070936	biological_process	protein K48-linked ubiquitination
B	0097602	molecular_function	cullin family protein binding
B	0140677	molecular_function	molecular function activator activity
B	0160072	molecular_function	ubiquitin ligase complex scaffold activity
B	1901524	biological_process	regulation of mitophagy
B	1904415	biological_process	regulation of xenophagy
B	1990444	molecular_function	F-box domain binding
B	1990756	molecular_function	ubiquitin-like ligase-substrate adaptor activity
B	1990757	molecular_function	ubiquitin ligase activator activity
B	2000001	biological_process	regulation of DNA damage checkpoint
C	0004842	molecular_function	ubiquitin-protein transferase activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0006508	biological_process	proteolysis
C	0016567	biological_process	protein ubiquitination
C	0019005	cellular_component	SCF ubiquitin ligase complex
C	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
C	0032496	biological_process	response to lipopolysaccharide
C	0050727	biological_process	regulation of inflammatory response
C	1990756	molecular_function	ubiquitin-like ligase-substrate adaptor activity
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

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	ILE749-ALA776

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Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	20
Details	Region: {"description":"Disordered","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

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site_id	SWS_FT_FI2
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"21406692","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

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site_id	SWS_FT_FI3
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1)","evidences":[{"source":"PubMed","id":"25114211","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	46
Details	Domain: {"description":"F-box","evidences":[{"source":"PROSITE-ProRule","id":"PRU00080","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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site_id	SWS_FT_FI5
Number of Residues	130
Details	Domain: {"description":"ApaG","evidences":[{"source":"PROSITE-ProRule","id":"PRU00412","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	60
Details	Domain: {"description":"Cullin neddylation","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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site_id	SWS_FT_FI7
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in NEDD8)","evidences":[{"source":"PubMed","id":"10597293","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15537541","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18805092","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

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