3TDZ

N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-stapled acetylated Ubc12N complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	EF-hand	8055669	3001983	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-hand	8055670	3001983	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	EF-hand	8055669	3001983	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	EF-hand	8055670	3001983	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003463	3000034	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Winged helix DNA-binding domain	8003463	3000034	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Cullin_binding	e3tdzA3	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: Cullin_binding	ECOD (1.6)
A	KOG3077	e3tdzA2	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: KOG3077	ECOD (1.6)
C [auth B]	Cullin_binding	e3tdzB3	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: Cullin_binding	ECOD (1.6)
C [auth B]	KOG3077	e3tdzB2	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: KOG3077	ECOD (1.6)
B [auth C]	Cullin_Nedd8	e3tdzC1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Cullin_Nedd8	ECOD (1.6)
D	Cullin_Nedd8	e3tdzD1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Cullin_Nedd8	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
C [auth B]	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
B [auth C]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
D	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B]	PF03556	Cullin binding (Cullin_binding)	Cullin binding	-	Family
B [auth C], D	PF10557	Cullin protein neddylation domain (Cullin_Nedd8)	Cullin protein neddylation domain	This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cu ...	This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae, and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B]	DCN1-like protein 1	protein binding binding ubiquitin-like protein binding ubiquitin-like protein conjugating enzyme binding enzyme binding ubiquitin conjugating enzyme binding cullin family protein binding	regulation of biological process organonitrogen compound metabolic process regulation of protein modification process regulation of post-translational protein modification regulation of protein metabolic process biological regulation regulation of protein ubiquitination primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process organic substance metabolic process protein ubiquitination macromolecule modification metabolic process regulation of biological process organonitrogen compound metabolic process regulation of protein modification process regulation of post-translational protein modification regulation of protein metabolic process biological regulation regulation of protein ubiquitination primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process organic substance metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process regulation of protein modification by small protein conjugation or removal protein modification process post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal protein neddylation regulation of protein neddylation positive regulation of protein metabolic process positive regulation of biological process positive regulation of post-translational protein modification positive regulation of metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein neddylation	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex
B [auth C], D	Cullin-1	ubiquitin ligase complex scaffold activity protein-macromolecule adaptor activity molecular adaptor activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction cellular process positive regulation of signaling developmental process anatomical structure morphogenesis animal organ development anatomical structure development animal organ morphogenesis cell death apoptotic signaling pathway apoptotic process intrinsic apoptotic signaling pathway programmed cell death cell population proliferation organonitrogen compound metabolic process primary metabolic process organic substance metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process organic substance catabolic process protein polyubiquitination protein K48-linked ubiquitination mitotic cell cycle process cell cycle phase transition cell cycle G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition cell cycle process protein monoubiquitination	cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane Parkin-FBXW7-Cul1 ubiquitin ligase complex cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane Parkin-FBXW7-Cul1 ubiquitin ligase complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen SCF ubiquitin ligase complex
E, F	STAPLED PEPTIDE	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding aminoacyltransferase activity ubiquitin-like protein transferase activity NEDD8 transferase activity catalytic activity, acting on a protein acyltransferase activity NEDD8 conjugating enzyme activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity ubiquitin-protein transferase activity	organic substance metabolic process organonitrogen compound metabolic process macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process regulation of biological process neuron apoptotic process positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process organic substance metabolic process organonitrogen compound metabolic process macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process regulation of biological process neuron apoptotic process positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process biological regulation positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process cellular process apoptotic process positive regulation of neuron apoptotic process programmed cell death positive regulation of cellular process regulation of neuron apoptotic process protein neddylation protein modification by small protein conjugation protein modification by small protein conjugation or removal	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR042460	DCN1-like, PONY binding domain	Homologous Superfamily
A, C [auth B]	IPR009060	UBA-like superfamily	Homologous Superfamily
A, C [auth B]	IPR005176	Potentiating neddylation domain	Domain
A, C [auth B]	IPR014764	Defective-in-cullin neddylation protein	Family
B [auth C], D	IPR045093	Cullin	Family
B [auth C], D	IPR019559	Cullin protein, neddylation domain	Domain
B [auth C], D	IPR016158	Cullin homology domain	Domain
B [auth C], D	IPR016157	Cullin, conserved site	Conserved Site
B [auth C], D	IPR001373	Cullin, N-terminal	Domain
B [auth C], D	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B [auth C], D	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
B [auth C], D	IPR036317	Cullin homology domain superfamily	Homologous Superfamily
B [auth C], D	IPR016159	Cullin repeat-like-containing domain superfamily	Homologous Superfamily
E, F	IPR000608	Ubiquitin-conjugating enzyme E2	Domain
E, F	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
E, F	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C [auth B]	Pharos: Q96GG9	breast cancer malignant mesothelioma osteosarcoma pituitary cancer sarcoidosis cancer myopathy ovarian cancer prostate carcinoma tuberculosis large cell medulloblastoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm rheumatoid arthritis
B [auth C], D	Pharos: Q13616	Stevens-Johnson syndrome Drug-Induced Stevens Johnson Syndrome ovarian cancer toxic epidermal necrolysis inflammatory bowel disease
E, F	Pharos: P61081	astrocytic tumor dermatomyositis oligodendroglioma psoriasis colorectal adenoma glioblastoma osteosarcoma colorectal cancer lung cancer plasma cell myeloma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E, F	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359
E, F	MK8	Parent Component: LEU RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354
E, F	MSE	Parent Component: MET RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.