6R7N

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	0001833	biological_process	inner cell mass cell proliferation
B	0001834	biological_process	trophectodermal cell proliferation
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	0035914	biological_process	skeletal muscle cell differentiation
B	0045116	biological_process	protein neddylation
B	0045892	biological_process	negative regulation of DNA-templated transcription
B	2000434	biological_process	regulation of protein neddylation
C	0000338	biological_process	protein deneddylation
C	0001701	biological_process	in utero embryonic development
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	0030054	cellular_component	cell junction
D	0031410	cellular_component	cytoplasmic vesicle
D	0032991	cellular_component	protein-containing complex
D	0045116	biological_process	protein neddylation
D	0045202	cellular_component	synapse
D	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	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	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	0030163	biological_process	protein catabolic process
O	0030674	molecular_function	protein-macromolecule adaptor activity
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	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
P	0006368	biological_process	transcription elongation by RNA polymerase II
P	0030891	cellular_component	VCB complex
P	0070449	cellular_component	elongin complex
Q	0000151	cellular_component	ubiquitin ligase complex
Q	0001222	molecular_function	transcription corepressor binding
Q	0005515	molecular_function	protein binding
Q	0005634	cellular_component	nucleus
Q	0005654	cellular_component	nucleoplasm
Q	0005737	cellular_component	cytoplasm
Q	0005829	cellular_component	cytosol
Q	0006357	biological_process	regulation of transcription by RNA polymerase II
Q	0006367	biological_process	transcription initiation at RNA polymerase II promoter
Q	0006511	biological_process	ubiquitin-dependent protein catabolic process
Q	0016567	biological_process	protein ubiquitination
Q	0030674	molecular_function	protein-macromolecule adaptor activity
Q	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
Q	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
Q	0070449	cellular_component	elongin complex
Q	0140958	biological_process	target-directed miRNA degradation
R	0008270	molecular_function	zinc ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	2
Details	binding site for residue ZN R 201

Chain	Residue
R	ASP51
R	LEU52

---

site_id	AC2
Number of Residues	6
Details	binding site for residue ZN R 202

Chain	Residue
R	ILE49
R	GLU66
R	GLU67
R	CYS68
R	THR69
R	VAL70

---

site_id	AC3
Number of Residues	3
Details	binding site for residue ZN R 203

Chain	Residue
R	PHE81
R	HIS82
R	GLU55

---

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	818
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	2
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	65
Details	Domain: {"description":"Ubiquitin-like","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
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_FI7
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P62869","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
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_FI9
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_FI10
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_FI11
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_FI12
Number of Residues	60
Details	Domain: {"description":"Cullin neddylation","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
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_FI14
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_FI15
Number of Residues	274
Details	Region: {"description":"Mediates interaction with NIF3L1","evidences":[{"source":"UniProtKB","id":"P61203","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---