6R6H

Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000338	biological_process	protein deneddylation
A	0005095	molecular_function	GTPase inhibitor activity
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	0007254	biological_process	JNK cascade
A	0008180	cellular_component	COP9 signalosome
A	0045116	biological_process	protein neddylation
A	2000434	biological_process	regulation of protein neddylation
B	0000122	biological_process	negative regulation of transcription by RNA polymerase II
B	0000338	biological_process	protein deneddylation
B	0003714	molecular_function	transcription corepressor activity
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	0006366	biological_process	transcription by RNA polymerase II
B	0006468	biological_process	protein phosphorylation
B	0007165	biological_process	signal transduction
B	0008180	cellular_component	COP9 signalosome
B	0030182	biological_process	neuron differentiation
B	0032991	cellular_component	protein-containing complex
B	0045116	biological_process	protein neddylation
B	0045171	cellular_component	intercellular bridge
B	2000434	biological_process	regulation of protein neddylation
C	0000338	biological_process	protein deneddylation
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	0006511	biological_process	ubiquitin-dependent protein catabolic process
C	0007165	biological_process	signal transduction
C	0008180	cellular_component	COP9 signalosome
C	0009416	biological_process	response to light stimulus
C	0043516	biological_process	regulation of DNA damage response, signal transduction by p53 class mediator
C	0045116	biological_process	protein neddylation
C	0048471	cellular_component	perinuclear region of cytoplasm
C	2000434	biological_process	regulation of protein neddylation
D	0000338	biological_process	protein deneddylation
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	0008021	cellular_component	synaptic vesicle
D	0008180	cellular_component	COP9 signalosome
D	0016607	cellular_component	nuclear speck
D	0019784	molecular_function	deNEDDylase activity
D	0031410	cellular_component	cytoplasmic vesicle
D	0032991	cellular_component	protein-containing complex
D	0045116	biological_process	protein neddylation
D	2000434	biological_process	regulation of protein neddylation
E	0000338	biological_process	protein deneddylation
E	0000785	cellular_component	chromatin
E	0003713	molecular_function	transcription coactivator activity
E	0003743	molecular_function	translation initiation factor activity
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0005852	cellular_component	eukaryotic translation initiation factor 3 complex
E	0006412	biological_process	translation
E	0006413	biological_process	translational initiation
E	0006508	biological_process	proteolysis
E	0008021	cellular_component	synaptic vesicle
E	0008180	cellular_component	COP9 signalosome
E	0008233	molecular_function	peptidase activity
E	0008237	molecular_function	metallopeptidase activity
E	0016787	molecular_function	hydrolase activity
E	0019784	molecular_function	deNEDDylase activity
E	0019899	molecular_function	enzyme binding
E	0031410	cellular_component	cytoplasmic vesicle
E	0035718	molecular_function	macrophage migration inhibitory factor binding
E	0043066	biological_process	negative regulation of apoptotic process
E	0043687	biological_process	post-translational protein modification
E	0045116	biological_process	protein neddylation
E	0045944	biological_process	positive regulation of transcription by RNA polymerase II
E	0046328	biological_process	regulation of JNK cascade
E	0046872	molecular_function	metal ion binding
E	0048471	cellular_component	perinuclear region of cytoplasm
E	0051091	biological_process	positive regulation of DNA-binding transcription factor activity
E	0051726	biological_process	regulation of cell cycle
E	0101005	molecular_function	deubiquitinase activity
E	0140492	molecular_function	metal-dependent deubiquitinase activity
E	1903894	biological_process	regulation of IRE1-mediated unfolded protein response
E	1990182	biological_process	exosomal secretion
E	2000434	biological_process	regulation of protein neddylation
F	0000338	biological_process	protein deneddylation
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0008180	cellular_component	COP9 signalosome
F	0008233	molecular_function	peptidase activity
F	0008237	molecular_function	metallopeptidase activity
F	0045116	biological_process	protein neddylation
F	0048471	cellular_component	perinuclear region of cytoplasm
F	0140492	molecular_function	metal-dependent deubiquitinase activity
F	2000434	biological_process	regulation of protein neddylation
G	0008180	cellular_component	COP9 signalosome
G	0010387	biological_process	COP9 signalosome assembly
H	0000338	biological_process	protein deneddylation
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0006468	biological_process	protein phosphorylation
H	0007250	biological_process	activation of NF-kappaB-inducing kinase activity
H	0008180	cellular_component	COP9 signalosome
H	0008285	biological_process	negative regulation of cell population proliferation
H	0010387	biological_process	COP9 signalosome assembly
H	0045116	biological_process	protein neddylation
H	0048471	cellular_component	perinuclear region of cytoplasm
H	0070062	cellular_component	extracellular exosome
H	2000434	biological_process	regulation of protein neddylation
O	0000082	biological_process	G1/S transition of mitotic cell cycle
O	0000122	biological_process	negative regulation of transcription by RNA polymerase II
O	0004842	molecular_function	ubiquitin-protein transferase activity
O	0005515	molecular_function	protein binding
O	0005634	cellular_component	nucleus
O	0005654	cellular_component	nucleoplasm
O	0005730	cellular_component	nucleolus
O	0005737	cellular_component	cytoplasm
O	0005829	cellular_component	cytosol
O	0006511	biological_process	ubiquitin-dependent protein catabolic process
O	0010498	biological_process	proteasomal protein catabolic process
O	0016567	biological_process	protein ubiquitination
O	0019005	cellular_component	SCF ubiquitin ligase complex
O	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
O	0031461	cellular_component	cullin-RING ubiquitin ligase complex
O	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
O	0031625	molecular_function	ubiquitin protein ligase binding
O	0031981	cellular_component	nuclear lumen
O	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
O	0072344	biological_process	rescue of stalled ribosome
O	0097193	biological_process	intrinsic apoptotic signaling pathway
O	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
O	0160072	molecular_function	ubiquitin ligase complex scaffold activity
O	0160276	biological_process	negative regulation of beige fat cell differentiation
O	1990116	biological_process	ribosome-associated ubiquitin-dependent protein catabolic process
O	2000104	biological_process	negative regulation of DNA-templated DNA replication
P	0006368	biological_process	transcription elongation by RNA polymerase II
P	0030891	cellular_component	VCB complex
P	0070449	cellular_component	elongin complex
Q	0000113	cellular_component	nucleotide-excision repair factor 4 complex
Q	0004842	molecular_function	ubiquitin-protein transferase activity
Q	0005515	molecular_function	protein binding
Q	0005634	cellular_component	nucleus
Q	0005737	cellular_component	cytoplasm
Q	0006289	biological_process	nucleotide-excision repair
Q	0006511	biological_process	ubiquitin-dependent protein catabolic process
Q	0009411	biological_process	response to UV
Q	0030674	molecular_function	protein-macromolecule adaptor activity
Q	0031463	cellular_component	Cul3-RING ubiquitin ligase complex
Q	0034644	biological_process	cellular response to UV
Q	0070449	cellular_component	elongin complex
Q	0070911	biological_process	global genome nucleotide-excision repair
R	0008270	molecular_function	zinc ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue ZN E 401

Chain	Residue
E	ARG106
E	ASN108
E	ILE150
E	ASP151
E	THR154

---

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
O	ILE718-ALA745

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	661
Details	Domain: {"description":"PCI","evidences":[{"source":"PROSITE-ProRule","id":"PRU01185","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18850735","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21406692","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	1
Details	Modified residue: {"description":"N-acetylalanine","evidences":[{"source":"PubMed","id":"18850735","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19413330","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
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_FI5
Number of Residues	270
Details	Domain: {"description":"MPN","evidences":[{"source":"PROSITE-ProRule","id":"PRU01182","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	13
Details	Motif: {"description":"JAMM motif","evidences":[{"source":"PROSITE-ProRule","id":"PRU01182","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01182","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	60
Details	Domain: {"description":"Cullin neddylation","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in NEDD8)","evidences":[{"source":"PubMed","id":"10092517","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10597293","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
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_FI12
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_FI13
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P62869","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"15665377","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	45
Details	Zinc finger: {"description":"RING-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00175","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
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_FI17
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_FI18
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_FI19
Number of Residues	55
Details	Region: {"description":"Involved in binding to CCT complex"}

Chain

Residue

Details

---

site_id	SWS_FT_FI20
Number of Residues	9
Details	Region: {"description":"Interaction with Elongin BC complex"}

Chain

Residue

Details

---