8R5H

Ubiquitin ligation to neosubstrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB-BRD4 BD2

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000082	biological_process	G1/S transition of mitotic cell cycle
A	0000122	biological_process	negative regulation of transcription by RNA polymerase II
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	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0010498	biological_process	proteasomal protein catabolic process
A	0016567	biological_process	protein ubiquitination
A	0019005	cellular_component	SCF ubiquitin ligase complex
A	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
A	0031461	cellular_component	cullin-RING ubiquitin ligase complex
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	0072344	biological_process	rescue of stalled ribosome
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
A	1990116	biological_process	ribosome-associated ubiquitin-dependent protein catabolic process
A	2000104	biological_process	negative regulation of DNA-templated DNA replication
D	0000122	biological_process	negative regulation of transcription by RNA polymerase II
D	0000151	cellular_component	ubiquitin ligase complex
D	0001222	molecular_function	transcription corepressor binding
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	0006351	biological_process	DNA-templated transcription
D	0006357	biological_process	regulation of transcription by RNA polymerase II
D	0006367	biological_process	transcription initiation at RNA polymerase II promoter
D	0006511	biological_process	ubiquitin-dependent protein catabolic process
D	0016567	biological_process	protein ubiquitination
D	0030674	molecular_function	protein-macromolecule adaptor activity
D	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
D	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
D	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
D	0070449	cellular_component	elongin complex
D	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
D	0140958	biological_process	target-directed miRNA degradation
D	1990116	biological_process	ribosome-associated ubiquitin-dependent protein catabolic process
D	2000104	biological_process	negative regulation of DNA-templated DNA replication
G	0000122	biological_process	negative regulation of transcription by RNA polymerase II
G	0000151	cellular_component	ubiquitin ligase complex
G	0001222	molecular_function	transcription corepressor binding
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005654	cellular_component	nucleoplasm
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0006351	biological_process	DNA-templated transcription
G	0006367	biological_process	transcription initiation at RNA polymerase II promoter
G	0006368	biological_process	transcription elongation by RNA polymerase II
G	0016567	biological_process	protein ubiquitination
G	0030891	cellular_component	VCB complex
G	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
G	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
G	0031625	molecular_function	ubiquitin protein ligase binding
G	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
G	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
G	0065003	biological_process	protein-containing complex assembly
G	0070449	cellular_component	elongin complex
G	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
G	0140958	biological_process	target-directed miRNA degradation
G	1990116	biological_process	ribosome-associated ubiquitin-dependent protein catabolic process
G	2000104	biological_process	negative regulation of DNA-templated DNA replication
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	PS00183
Number of Residues	16
Details	UBC_1 Ubiquitin-conjugating (UBC) active site signature. WHPNIyen.GdVCIsiL

Chain	Residue	Details
C	TRP82-LEU97

---

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

Chain	Residue	Details
U	LYS27-ASP52

---

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	1
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	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":"8Q7H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8RHZ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	4
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_FI4
Number of Residues	1
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

---

site_id	SWS_FT_FI5
Number of Residues	166
Details	Domain: {"description":"UBC core","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	15
Details	Region: {"description":"Important for ubiquitin transfer","evidences":[{"source":"PubMed","id":"38326650","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"38326650","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8PQL","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	1
Details	Site: {"description":"Acetylated histone binding","evidences":[{"source":"PubMed","id":"22464331","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	65
Details	Domain: {"description":"Ubiquitin-like","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	1
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_FI11
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P62869","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	55
Details	Region: {"description":"Involved in binding to CCT complex"}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	9
Details	Region: {"description":"Interaction with Elongin BC complex"}

Chain

Residue

Details

---