6R7I

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	0032991	cellular_component	protein-containing complex
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	0032991	cellular_component	protein-containing complex
C	0045116	biological_process	protein neddylation
C	0048471	cellular_component	perinuclear region of cytoplasm
C	1902162	biological_process	regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator
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
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	0016579	biological_process	protein deubiquitination
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	0045202	cellular_component	synapse
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	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
N	0005515	molecular_function	protein binding
N	0005634	cellular_component	nucleus
N	0005654	cellular_component	nucleoplasm
N	0005737	cellular_component	cytoplasm
N	0005829	cellular_component	cytosol
N	0006357	biological_process	regulation of transcription by RNA polymerase II
N	0006508	biological_process	proteolysis
N	0006511	biological_process	ubiquitin-dependent protein catabolic process
N	0008104	biological_process	protein localization
N	0009653	biological_process	anatomical structure morphogenesis
N	0016567	biological_process	protein ubiquitination
N	0019941	biological_process	modification-dependent protein catabolic process
N	0030162	biological_process	regulation of proteolysis
N	0031386	molecular_function	protein tag activity
N	0031625	molecular_function	ubiquitin protein ligase binding
N	0036211	biological_process	protein modification process
N	0045116	biological_process	protein neddylation
N	0070062	cellular_component	extracellular exosome
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	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	0030891	cellular_component	VCB 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	0044877	molecular_function	protein-containing complex binding
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	0001222	molecular_function	transcription corepressor binding
P	0005515	molecular_function	protein binding
P	0005634	cellular_component	nucleus
P	0005654	cellular_component	nucleoplasm
P	0005829	cellular_component	cytosol
P	0006367	biological_process	transcription initiation at RNA polymerase II promoter
P	0006368	biological_process	transcription elongation by RNA polymerase II
P	0016567	biological_process	protein ubiquitination
P	0030891	cellular_component	VCB complex
P	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
P	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
P	0031625	molecular_function	ubiquitin protein ligase binding
P	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
P	0065003	biological_process	protein-containing complex assembly
P	0070449	cellular_component	elongin complex
P	0140958	biological_process	target-directed miRNA degradation
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	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

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site_id	AC2
Number of Residues	5
Details	binding site for residue ZN R 201

Chain	Residue
R	ILE54
R	ASN47
R	ASP51
R	LEU52
R	CYS53

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site_id	AC3
Number of Residues	4
Details	binding site for residue ZN R 202

Chain	Residue
R	CYS42
R	ILE49
R	THR69
R	ALA78

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site_id	AC4
Number of Residues	1
Details	binding site for residue ZN R 203

Chain	Residue
R	HIS82

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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

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

Chain	Residue	Details
N	LYS127-ASP152

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Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	45
Details	ZN_FING: RING-type => ECO:0000255|PROSITE-ProRule:PRU00175

Chain	Residue	Details
R	CYS53-ASN98
N	ILE144
E	ASP151

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site_id	SWS_FT_FI2
Number of Residues	11
Details	BINDING: BINDING => ECO:0000269|PubMed:11961546, ECO:0007744|PDB:1LDJ, ECO:0007744|PDB:1LDK, ECO:0007744|PDB:1U6G, ECO:0007744|PDB:2HYE, ECO:0007744|PDB:3DPL, ECO:0007744|PDB:3DQV, ECO:0007744|PDB:3RTR, ECO:0007744|PDB:4F52, ECO:0007744|PDB:4P5O

Chain	Residue	Details
R	CYS42
R	CYS94
R	ASP97
R	CYS45
R	CYS53
R	CYS56
R	CYS68
R	CYS75
R	HIS77
R	HIS80
R	HIS82

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site_id	SWS_FT_FI3
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269|PubMed:11961546, ECO:0007744|PDB:1LDJ, ECO:0007744|PDB:1LDK, ECO:0007744|PDB:1U6G, ECO:0007744|PDB:2HYE, ECO:0007744|PDB:3DQV, ECO:0007744|PDB:3RTR, ECO:0007744|PDB:4F52, ECO:0007744|PDB:4P5O

Chain	Residue	Details
R	CYS83

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site_id	SWS_FT_FI4
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Chain	Residue	Details
N	GLY176

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