Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4D10

Crystal structure of 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
I	0000338	biological_process	protein deneddylation
I	0005095	molecular_function	GTPase inhibitor activity
I	0005515	molecular_function	protein binding
I	0005634	cellular_component	nucleus
I	0005654	cellular_component	nucleoplasm
I	0005737	cellular_component	cytoplasm
I	0005829	cellular_component	cytosol
I	0007254	biological_process	JNK cascade
I	0008180	cellular_component	COP9 signalosome
I	0045116	biological_process	protein neddylation
I	2000434	biological_process	regulation of protein neddylation
J	0000122	biological_process	negative regulation of transcription by RNA polymerase II
J	0000338	biological_process	protein deneddylation
J	0003714	molecular_function	transcription corepressor activity
J	0005515	molecular_function	protein binding
J	0005634	cellular_component	nucleus
J	0005654	cellular_component	nucleoplasm
J	0005737	cellular_component	cytoplasm
J	0005829	cellular_component	cytosol
J	0006366	biological_process	transcription by RNA polymerase II
J	0006468	biological_process	protein phosphorylation
J	0007165	biological_process	signal transduction
J	0008180	cellular_component	COP9 signalosome
J	0030182	biological_process	neuron differentiation
J	0032991	cellular_component	protein-containing complex
J	0045116	biological_process	protein neddylation
J	0045171	cellular_component	intercellular bridge
J	2000434	biological_process	regulation of protein neddylation
K	0000338	biological_process	protein deneddylation
K	0005515	molecular_function	protein binding
K	0005634	cellular_component	nucleus
K	0005654	cellular_component	nucleoplasm
K	0005737	cellular_component	cytoplasm
K	0005829	cellular_component	cytosol
K	0006511	biological_process	ubiquitin-dependent protein catabolic process
K	0007165	biological_process	signal transduction
K	0008180	cellular_component	COP9 signalosome
K	0009416	biological_process	response to light stimulus
K	0043516	biological_process	regulation of DNA damage response, signal transduction by p53 class mediator
K	0045116	biological_process	protein neddylation
K	0048471	cellular_component	perinuclear region of cytoplasm
K	2000434	biological_process	regulation of protein neddylation
L	0000338	biological_process	protein deneddylation
L	0005515	molecular_function	protein binding
L	0005634	cellular_component	nucleus
L	0005654	cellular_component	nucleoplasm
L	0005737	cellular_component	cytoplasm
L	0005829	cellular_component	cytosol
L	0008021	cellular_component	synaptic vesicle
L	0008180	cellular_component	COP9 signalosome
L	0016607	cellular_component	nuclear speck
L	0019784	molecular_function	deNEDDylase activity
L	0031410	cellular_component	cytoplasmic vesicle
L	0032991	cellular_component	protein-containing complex
L	0045116	biological_process	protein neddylation
L	2000434	biological_process	regulation of protein neddylation
M	0000338	biological_process	protein deneddylation
M	0000785	cellular_component	chromatin
M	0003713	molecular_function	transcription coactivator activity
M	0003743	molecular_function	translation initiation factor activity
M	0005515	molecular_function	protein binding
M	0005634	cellular_component	nucleus
M	0005654	cellular_component	nucleoplasm
M	0005737	cellular_component	cytoplasm
M	0005829	cellular_component	cytosol
M	0005852	cellular_component	eukaryotic translation initiation factor 3 complex
M	0006412	biological_process	translation
M	0006413	biological_process	translational initiation
M	0006508	biological_process	proteolysis
M	0008021	cellular_component	synaptic vesicle
M	0008180	cellular_component	COP9 signalosome
M	0008233	molecular_function	peptidase activity
M	0008237	molecular_function	metallopeptidase activity
M	0016787	molecular_function	hydrolase activity
M	0019784	molecular_function	deNEDDylase activity
M	0019899	molecular_function	enzyme binding
M	0031410	cellular_component	cytoplasmic vesicle
M	0035718	molecular_function	macrophage migration inhibitory factor binding
M	0043066	biological_process	negative regulation of apoptotic process
M	0043687	biological_process	post-translational protein modification
M	0045116	biological_process	protein neddylation
M	0045944	biological_process	positive regulation of transcription by RNA polymerase II
M	0046328	biological_process	regulation of JNK cascade
M	0046872	molecular_function	metal ion binding
M	0048471	cellular_component	perinuclear region of cytoplasm
M	0051091	biological_process	positive regulation of DNA-binding transcription factor activity
M	0051726	biological_process	regulation of cell cycle
M	0101005	molecular_function	deubiquitinase activity
M	0140492	molecular_function	metal-dependent deubiquitinase activity
M	1903894	biological_process	regulation of IRE1-mediated unfolded protein response
M	1990182	biological_process	exosomal secretion
M	2000434	biological_process	regulation of protein neddylation
N	0000338	biological_process	protein deneddylation
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	0008180	cellular_component	COP9 signalosome
N	0008233	molecular_function	peptidase activity
N	0008237	molecular_function	metallopeptidase activity
N	0045116	biological_process	protein neddylation
N	0048471	cellular_component	perinuclear region of cytoplasm
N	0140492	molecular_function	metal-dependent deubiquitinase activity
N	2000434	biological_process	regulation of protein neddylation
O	0008180	cellular_component	COP9 signalosome
O	0010387	biological_process	COP9 signalosome assembly
P	0000338	biological_process	protein deneddylation
P	0005515	molecular_function	protein binding
P	0005634	cellular_component	nucleus
P	0005654	cellular_component	nucleoplasm
P	0005737	cellular_component	cytoplasm
P	0005829	cellular_component	cytosol
P	0006468	biological_process	protein phosphorylation
P	0007250	biological_process	activation of NF-kappaB-inducing kinase activity
P	0008180	cellular_component	COP9 signalosome
P	0008285	biological_process	negative regulation of cell population proliferation
P	0010387	biological_process	COP9 signalosome assembly
P	0045116	biological_process	protein neddylation
P	0048471	cellular_component	perinuclear region of cytoplasm
P	0070062	cellular_component	extracellular exosome
P	2000434	biological_process	regulation of protein neddylation

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN E 999

Chain	Residue
E	GLU104
E	HIS138
E	HIS140
E	ASP151

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN M 999

Chain	Residue
M	GLU104
M	HIS138
M	HIS140
M	ASP151

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1322
Details	Domain: {"description":"PCI","evidences":[{"source":"PROSITE-ProRule","id":"PRU01185","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	2
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	1
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	540
Details	Domain: {"description":"MPN","evidences":[{"source":"PROSITE-ProRule","id":"PRU01182","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	26
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	6
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01182","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)