9J63

Cryo-EM structure of neddylated Cul2-Rbx1-EloBC-FEM1B homodimer

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000082	biological_process	G1/S transition of mitotic cell cycle
A	0004842	molecular_function	ubiquitin-protein transferase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005730	cellular_component	nucleolus
A	0005829	cellular_component	cytosol
A	0010498	biological_process	proteasomal protein catabolic process
A	0016567	biological_process	protein ubiquitination
A	0019005	cellular_component	SCF ubiquitin ligase complex
A	0030163	biological_process	protein catabolic process
A	0030674	molecular_function	protein-macromolecule adaptor activity
A	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
A	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
A	0031625	molecular_function	ubiquitin protein ligase binding
A	0031981	cellular_component	nuclear lumen
A	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
A	0097193	biological_process	intrinsic apoptotic signaling pathway
A	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
A	0160072	molecular_function	ubiquitin ligase complex scaffold activity
A	0160276	biological_process	negative regulation of beige fat cell differentiation
D	0000082	biological_process	G1/S transition of mitotic cell cycle
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	0005730	cellular_component	nucleolus
D	0005829	cellular_component	cytosol
D	0010498	biological_process	proteasomal protein catabolic process
D	0016567	biological_process	protein ubiquitination
D	0019005	cellular_component	SCF ubiquitin ligase complex
D	0030163	biological_process	protein catabolic process
D	0030674	molecular_function	protein-macromolecule adaptor activity
D	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
D	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
D	0031625	molecular_function	ubiquitin protein ligase binding
D	0031981	cellular_component	nuclear lumen
D	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
D	0097193	biological_process	intrinsic apoptotic signaling pathway
D	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
D	0160072	molecular_function	ubiquitin ligase complex scaffold activity
D	0160276	biological_process	negative regulation of beige fat cell differentiation
E	0000165	biological_process	MAPK cascade
E	0000209	biological_process	protein polyubiquitination
E	0004842	molecular_function	ubiquitin-protein transferase activity
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005737	cellular_component	cytoplasm
E	0005813	cellular_component	centrosome
E	0005829	cellular_component	cytosol
E	0006281	biological_process	DNA repair
E	0006283	biological_process	transcription-coupled nucleotide-excision repair
E	0006511	biological_process	ubiquitin-dependent protein catabolic process
E	0006513	biological_process	protein monoubiquitination
E	0006974	biological_process	DNA damage response
E	0007283	biological_process	spermatogenesis
E	0008270	molecular_function	zinc ion binding
E	0016567	biological_process	protein ubiquitination
E	0016740	molecular_function	transferase activity
E	0019005	cellular_component	SCF ubiquitin ligase complex
E	0019788	molecular_function	NEDD8 transferase activity
E	0030163	biological_process	protein catabolic process
E	0030891	cellular_component	VCB complex
E	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
E	0031461	cellular_component	cullin-RING ubiquitin ligase complex
E	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
E	0031463	cellular_component	Cul3-RING ubiquitin ligase complex
E	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
E	0031465	cellular_component	Cul4B-RING E3 ubiquitin ligase complex
E	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
E	0031467	cellular_component	Cul7-RING ubiquitin ligase complex
E	0031625	molecular_function	ubiquitin protein ligase binding
E	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
E	0032480	biological_process	negative regulation of type I interferon production
E	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
E	0034599	biological_process	cellular response to oxidative stress
E	0034644	biological_process	cellular response to UV
E	0042110	biological_process	T cell activation
E	0042770	biological_process	signal transduction in response to DNA damage
E	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
E	0043124	biological_process	negative regulation of canonical NF-kappaB signal transduction
E	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
E	0043687	biological_process	post-translational protein modification
E	0044314	biological_process	protein K27-linked ubiquitination
E	0044877	molecular_function	protein-containing complex binding
E	0045116	biological_process	protein neddylation
E	0045732	biological_process	positive regulation of protein catabolic process
E	0046627	biological_process	negative regulation of insulin receptor signaling pathway
E	0046872	molecular_function	metal ion binding
E	0060090	molecular_function	molecular adaptor activity
E	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
E	0061630	molecular_function	ubiquitin protein ligase activity
E	0061663	molecular_function	NEDD8 ligase activity
E	0062197	biological_process	cellular response to chemical stress
E	0070936	biological_process	protein K48-linked ubiquitination
E	0071230	biological_process	cellular response to amino acid stimulus
E	0080008	cellular_component	Cul4-RING E3 ubiquitin ligase complex
E	0090090	biological_process	negative regulation of canonical Wnt signaling pathway
E	0090734	cellular_component	site of DNA damage
E	0097602	molecular_function	cullin family protein binding
E	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
E	0160240	biological_process	RNA polymerase II transcription initiation surveillance
E	0160276	biological_process	negative regulation of beige fat cell differentiation
E	1900076	biological_process	regulation of cellular response to insulin stimulus
E	1901525	biological_process	negative regulation of mitophagy
E	1902499	biological_process	positive regulation of protein autoubiquitination
E	1902883	biological_process	negative regulation of response to oxidative stress
E	1904263	biological_process	positive regulation of TORC1 signaling
H	0000165	biological_process	MAPK cascade
H	0000209	biological_process	protein polyubiquitination
H	0004842	molecular_function	ubiquitin-protein transferase activity
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0005737	cellular_component	cytoplasm
H	0005813	cellular_component	centrosome
H	0005829	cellular_component	cytosol
H	0006281	biological_process	DNA repair
H	0006283	biological_process	transcription-coupled nucleotide-excision repair
H	0006511	biological_process	ubiquitin-dependent protein catabolic process
H	0006513	biological_process	protein monoubiquitination
H	0006974	biological_process	DNA damage response
H	0007283	biological_process	spermatogenesis
H	0008270	molecular_function	zinc ion binding
H	0016567	biological_process	protein ubiquitination
H	0016740	molecular_function	transferase activity
H	0019005	cellular_component	SCF ubiquitin ligase complex
H	0019788	molecular_function	NEDD8 transferase activity
H	0030163	biological_process	protein catabolic process
H	0030891	cellular_component	VCB complex
H	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
H	0031461	cellular_component	cullin-RING ubiquitin ligase complex
H	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
H	0031463	cellular_component	Cul3-RING ubiquitin ligase complex
H	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
H	0031465	cellular_component	Cul4B-RING E3 ubiquitin ligase complex
H	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
H	0031467	cellular_component	Cul7-RING ubiquitin ligase complex
H	0031625	molecular_function	ubiquitin protein ligase binding
H	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
H	0032480	biological_process	negative regulation of type I interferon production
H	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
H	0034599	biological_process	cellular response to oxidative stress
H	0034644	biological_process	cellular response to UV
H	0042110	biological_process	T cell activation
H	0042770	biological_process	signal transduction in response to DNA damage
H	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
H	0043124	biological_process	negative regulation of canonical NF-kappaB signal transduction
H	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
H	0043687	biological_process	post-translational protein modification
H	0044314	biological_process	protein K27-linked ubiquitination
H	0044877	molecular_function	protein-containing complex binding
H	0045116	biological_process	protein neddylation
H	0045732	biological_process	positive regulation of protein catabolic process
H	0046627	biological_process	negative regulation of insulin receptor signaling pathway
H	0046872	molecular_function	metal ion binding
H	0060090	molecular_function	molecular adaptor activity
H	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
H	0061630	molecular_function	ubiquitin protein ligase activity
H	0061663	molecular_function	NEDD8 ligase activity
H	0062197	biological_process	cellular response to chemical stress
H	0070936	biological_process	protein K48-linked ubiquitination
H	0071230	biological_process	cellular response to amino acid stimulus
H	0080008	cellular_component	Cul4-RING E3 ubiquitin ligase complex
H	0090090	biological_process	negative regulation of canonical Wnt signaling pathway
H	0090734	cellular_component	site of DNA damage
H	0097602	molecular_function	cullin family protein binding
H	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
H	0160240	biological_process	RNA polymerase II transcription initiation surveillance
H	0160276	biological_process	negative regulation of beige fat cell differentiation
H	1900076	biological_process	regulation of cellular response to insulin stimulus
H	1901525	biological_process	negative regulation of mitophagy
H	1902499	biological_process	positive regulation of protein autoubiquitination
H	1902883	biological_process	negative regulation of response to oxidative stress
H	1904263	biological_process	positive regulation of TORC1 signaling

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	ILE718-ALA745

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	Modified residue: {"description":"N-acetylmethionine","evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAR-2009","submissionDatabase":"UniProtKB","authors":["Bienvenut W.V.","Waridel P.","Quadroni M."]}},{"source":"PubMed","id":"19413330","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"22814378","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
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_FI4
Number of Residues	7
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_FI5
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

---