8H38

Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex

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
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	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	0000338	biological_process	protein deneddylation
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	0008180	cellular_component	COP9 signalosome
G	0010387	biological_process	COP9 signalosome assembly
G	0032991	cellular_component	protein-containing complex
G	2000434	biological_process	regulation of protein neddylation
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	0005737	cellular_component	cytoplasm
I	0006006	biological_process	glucose metabolic process
I	0006629	biological_process	lipid metabolic process
I	0010467	biological_process	gene expression
I	0016567	biological_process	protein ubiquitination
I	0031463	cellular_component	Cul3-RING ubiquitin ligase complex
I	0032868	biological_process	response to insulin
I	0032869	biological_process	cellular response to insulin stimulus
I	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
I	0043491	biological_process	phosphatidylinositol 3-kinase/protein kinase B signal transduction
I	0070936	biological_process	protein K48-linked ubiquitination
I	1900076	biological_process	regulation of cellular response to insulin stimulus
I	1990756	molecular_function	ubiquitin-like ligase-substrate adaptor activity
L	0000082	biological_process	G1/S transition of mitotic cell cycle
L	0000122	biological_process	negative regulation of transcription by RNA polymerase II
L	0000209	biological_process	protein polyubiquitination
L	0000278	biological_process	mitotic cell cycle
L	0000902	biological_process	cell morphogenesis
L	0000922	cellular_component	spindle pole
L	0001701	biological_process	in utero embryonic development
L	0001822	biological_process	kidney development
L	0001831	biological_process	trophectodermal cellular morphogenesis
L	0004842	molecular_function	ubiquitin-protein transferase activity
L	0005112	molecular_function	Notch binding
L	0005515	molecular_function	protein binding
L	0005634	cellular_component	nucleus
L	0005654	cellular_component	nucleoplasm
L	0005737	cellular_component	cytoplasm
L	0005794	cellular_component	Golgi apparatus
L	0005813	cellular_component	centrosome
L	0005819	cellular_component	spindle
L	0005827	cellular_component	polar microtubule
L	0005829	cellular_component	cytosol
L	0005856	cellular_component	cytoskeleton
L	0005886	cellular_component	plasma membrane
L	0005929	cellular_component	cilium
L	0006357	biological_process	regulation of transcription by RNA polymerase II
L	0006366	biological_process	transcription by RNA polymerase II
L	0006368	biological_process	transcription elongation by RNA polymerase II
L	0006511	biological_process	ubiquitin-dependent protein catabolic process
L	0006513	biological_process	protein monoubiquitination
L	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
L	0006888	biological_process	endoplasmic reticulum to Golgi vesicle-mediated transport
L	0006915	biological_process	apoptotic process
L	0006950	biological_process	response to stress
L	0006954	biological_process	inflammatory response
L	0006979	biological_process	response to oxidative stress
L	0007080	biological_process	mitotic metaphase chromosome alignment
L	0007165	biological_process	signal transduction
L	0007229	biological_process	integrin-mediated signaling pathway
L	0007369	biological_process	gastrulation
L	0008284	biological_process	positive regulation of cell population proliferation
L	0010467	biological_process	gene expression
L	0010468	biological_process	regulation of gene expression
L	0010558	biological_process	negative regulation of macromolecule biosynthetic process
L	0016020	cellular_component	membrane
L	0016055	biological_process	Wnt signaling pathway
L	0016192	biological_process	vesicle-mediated transport
L	0016477	biological_process	cell migration
L	0016567	biological_process	protein ubiquitination
L	0017145	biological_process	stem cell division
L	0030030	biological_process	cell projection organization
L	0030163	biological_process	protein catabolic process
L	0030332	molecular_function	cyclin binding
L	0031145	biological_process	anaphase-promoting complex-dependent catabolic process
L	0031208	molecular_function	POZ domain binding
L	0031398	biological_process	positive regulation of protein ubiquitination
L	0031461	cellular_component	cullin-RING ubiquitin ligase complex
L	0031463	cellular_component	Cul3-RING ubiquitin ligase complex
L	0031514	cellular_component	motile cilium
L	0031625	molecular_function	ubiquitin protein ligase binding
L	0031648	biological_process	protein destabilization
L	0031669	biological_process	cellular response to nutrient levels
L	0032467	biological_process	positive regulation of cytokinesis
L	0032480	biological_process	negative regulation of type I interferon production
L	0032481	biological_process	positive regulation of type I interferon production
L	0032869	biological_process	cellular response to insulin stimulus
L	0034198	biological_process	cellular response to amino acid starvation
L	0034599	biological_process	cellular response to oxidative stress
L	0035024	biological_process	negative regulation of Rho protein signal transduction
L	0036126	cellular_component	sperm flagellum
L	0040016	biological_process	embryonic cleavage
L	0042802	molecular_function	identical protein binding
L	0042995	cellular_component	cell projection
L	0043149	biological_process	stress fiber assembly
L	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
L	0044346	biological_process	fibroblast apoptotic process
L	0045842	biological_process	positive regulation of mitotic metaphase/anaphase transition
L	0048208	biological_process	COPII vesicle coating
L	0051301	biological_process	cell division
L	0051865	biological_process	protein autoubiquitination
L	0060337	biological_process	type I interferon-mediated signaling pathway
L	0061630	molecular_function	ubiquitin protein ligase activity
L	0070062	cellular_component	extracellular exosome
L	0070294	biological_process	renal sodium ion absorption
L	0070936	biological_process	protein K48-linked ubiquitination
L	0071230	biological_process	cellular response to amino acid stimulus
L	0071630	biological_process	nuclear protein quality control by the ubiquitin-proteasome system
L	0072576	biological_process	liver morphogenesis
L	0072686	cellular_component	mitotic spindle
L	0080090	biological_process	regulation of primary metabolic process
L	0097193	biological_process	intrinsic apoptotic signaling pathway
L	0098794	cellular_component	postsynapse
L	0098978	cellular_component	glutamatergic synapse
L	0140252	biological_process	regulation protein catabolic process at postsynapse
L	0160072	molecular_function	ubiquitin ligase complex scaffold activity
L	0160240	biological_process	RNA polymerase II transcription initiation surveillance
L	1900076	biological_process	regulation of cellular response to insulin stimulus
L	1901992	biological_process	positive regulation of mitotic cell cycle phase transition
L	1904262	biological_process	negative regulation of TORC1 signaling
L	1904263	biological_process	positive regulation of TORC1 signaling
M	0005737	cellular_component	cytoplasm
M	0006006	biological_process	glucose metabolic process
M	0006629	biological_process	lipid metabolic process
M	0010467	biological_process	gene expression
M	0016567	biological_process	protein ubiquitination
M	0031463	cellular_component	Cul3-RING ubiquitin ligase complex
M	0032868	biological_process	response to insulin
M	0032869	biological_process	cellular response to insulin stimulus
M	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
M	0043491	biological_process	phosphatidylinositol 3-kinase/protein kinase B signal transduction
M	0070936	biological_process	protein K48-linked ubiquitination
M	1900076	biological_process	regulation of cellular response to insulin stimulus
M	1990756	molecular_function	ubiquitin-like ligase-substrate adaptor activity
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
N	0072757	biological_process	cellular response to camptothecin
N	0098794	cellular_component	postsynapse
N	0098978	cellular_component	glutamatergic synapse
N	0150052	biological_process	regulation of postsynapse assembly
R	0000045	biological_process	autophagosome assembly
R	0000082	biological_process	G1/S transition of mitotic cell cycle
R	0000165	biological_process	MAPK cascade
R	0000209	biological_process	protein polyubiquitination
R	0000423	biological_process	mitophagy
R	0001837	biological_process	epithelial to mesenchymal transition
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	0005829	cellular_component	cytosol
R	0006281	biological_process	DNA repair
R	0006283	biological_process	transcription-coupled nucleotide-excision repair
R	0006366	biological_process	transcription by RNA polymerase II
R	0006368	biological_process	transcription elongation by RNA polymerase II
R	0006511	biological_process	ubiquitin-dependent protein catabolic process
R	0006513	biological_process	protein monoubiquitination
R	0006915	biological_process	apoptotic process
R	0006974	biological_process	DNA damage response
R	0006979	biological_process	response to oxidative stress
R	0007040	biological_process	lysosome organization
R	0007283	biological_process	spermatogenesis
R	0007346	biological_process	regulation of mitotic cell cycle
R	0008270	molecular_function	zinc ion binding
R	0008286	biological_process	insulin receptor signaling pathway
R	0010507	biological_process	negative regulation of autophagy
R	0010508	biological_process	positive regulation of autophagy
R	0016567	biological_process	protein ubiquitination
R	0016740	molecular_function	transferase activity
R	0019005	cellular_component	SCF ubiquitin ligase complex
R	0019221	biological_process	cytokine-mediated signaling pathway
R	0019788	molecular_function	NEDD8 transferase activity
R	0030163	biological_process	protein catabolic process
R	0030330	biological_process	DNA damage response, signal transduction by p53 class mediator
R	0030891	cellular_component	VCB complex
R	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
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	0031669	biological_process	cellular response to nutrient levels
R	0032435	biological_process	negative regulation of proteasomal ubiquitin-dependent protein catabolic process
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	0032481	biological_process	positive regulation of type I interferon production
R	0032869	biological_process	cellular response to insulin stimulus
R	0034198	biological_process	cellular response to amino acid starvation
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	0035279	biological_process	miRNA-mediated gene silencing by mRNA destabilization
R	0038066	biological_process	p38MAPK cascade
R	0038202	biological_process	TORC1 signaling
R	0042110	biological_process	T cell activation
R	0042770	biological_process	signal transduction in response to DNA damage
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	0044877	molecular_function	protein-containing complex binding
R	0045116	biological_process	protein neddylation
R	0045727	biological_process	positive regulation of translation
R	0045732	biological_process	positive regulation of protein catabolic process
R	0045944	biological_process	positive regulation of transcription by RNA polymerase II
R	0046627	biological_process	negative regulation of insulin receptor signaling pathway
R	0046872	molecular_function	metal ion binding
R	0060090	molecular_function	molecular adaptor activity
R	0060337	biological_process	type I interferon-mediated signaling pathway
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	0070294	biological_process	renal sodium ion absorption
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	0090090	biological_process	negative regulation of canonical Wnt signaling pathway
R	0090734	cellular_component	site of DNA damage
R	0097510	biological_process	base-excision repair, AP site formation via deaminated base removal
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	1900076	biological_process	regulation of cellular response to insulin stimulus
R	1901525	biological_process	negative regulation of mitophagy
R	1901797	biological_process	negative regulation of signal transduction by p53 class mediator
R	1902499	biological_process	positive regulation of protein autoubiquitination
R	1902883	biological_process	negative regulation of response to oxidative stress
R	1904037	biological_process	positive regulation of epithelial cell apoptotic process
R	1904262	biological_process	negative regulation of TORC1 signaling
R	1904263	biological_process	positive regulation of TORC1 signaling
R	2000059	biological_process	negative regulation of ubiquitin-dependent protein catabolic process

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
N	LYS27-ASP52

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

Chain	Residue	Details
L	ILE741-ALA768

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Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	SITE: Interaction with UBE1C => ECO:0000269|PubMed:14690597

Chain	Residue	Details
N	LEU8
N	ILE44
E	ASP151

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site_id	SWS_FT_FI2
Number of Residues	1
Details	MOD_RES: (Microbial infection) Deamidated glutamine => ECO:0000269|PubMed:20688984, ECO:0000269|PubMed:21903097, ECO:0000269|PubMed:23175788, ECO:0000269|PubMed:23589306, ECO:0000269|PubMed:26632597

Chain	Residue	Details
N	GLN40
R	CYS45
R	CYS75
R	HIS77
R	HIS80
R	CYS94
R	ASP97

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site_id	SWS_FT_FI3
Number of Residues	1
Details	MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P29595

Chain	Residue	Details
N	LYS48
R	CYS56
R	CYS68
R	HIS82

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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) => ECO:0000269|PubMed:38316879

Chain	Residue	Details
N	GLY76

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site_id	SWS_FT_FI5
Number of Residues	1
Details	MOD_RES: N-acetylmethionine => ECO:0007744|PubMed:20068231

Chain	Residue	Details
R	MET1

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site_id	SWS_FT_FI6
Number of Residues	1
Details	MOD_RES: N-acetylalanine; in E3 ubiquitin-protein ligase RBX1, N-terminally processed => ECO:0000269|Ref.8, ECO:0007744|PubMed:19413330, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:22223895, ECO:0007744|PubMed:22814378

Chain	Residue	Details
R	ALA2

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site_id	SWS_FT_FI7
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163

Chain	Residue	Details
R	THR9

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