3O6B | pdb_00003o6b

A Dual E3 Mechanism for Rub1 Ligation to Cdc53: Dcn1(P)-Cdc53(WHB) low resolution

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Winged helix DNA-binding domain	8088860	3000034	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Winged helix DNA-binding domain	8088860	3000034	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Winged helix DNA-binding domain	8088860	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8088860	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-hand	8055667	3001983	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-hand	8055668	3001983	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	EF-hand	8055667	3001983	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	EF-hand	8055668	3001983	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	EF-hand	8055668	3001983	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	EF-hand	8055667	3001983	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	EF-hand	8055668	3001983	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EF-hand	8055668	3001983	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EF-hand	8055667	3001983	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)
D		e3o6bD3	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: PCI	F:	ECOD (20:10:01)
F		e3o6bF2	A: Fusion glycoprotein F2	X: Fusion glycoprotein F2	H: Fusion glycoprotein F2	T:	F:	ECOD (20:10:01)
J		e3o6bJ3	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: PCI	F:	ECOD (20:10:01)
H		e3o6bH3	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: PCI	F:	ECOD (20:10:01)
B		e3o6bB3	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: PCI	F:	ECOD (20:10:01)
A		e3o6bA2	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T:	F:	ECOD (20:10:01)
A		e3o6bA3	A: RuvA-C	X: post-HMGL domain-like	H: post-HMGL domain-like	T: Cobalamin_bind	F:	ECOD (20:10:01)
E		e3o6bE2	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T:	F:	ECOD (20:10:01)
E		e3o6bE3	A: RuvA-C	X: post-HMGL domain-like	H: post-HMGL domain-like	T: Cobalamin_bind	F:	ECOD (20:10:01)
G		e3o6bG2	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T:	F:	ECOD (20:10:01)
G		e3o6bG3	A: RuvA-C	X: post-HMGL domain-like	H: post-HMGL domain-like	T: Cobalamin_bind	F:	ECOD (20:10:01)
I		e3o6bI2	A: HTH	X: HTH	H: winged helix domain	T: PI3K_C2	F:	ECOD (20:10:01)
C		e3o6bC2	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T:	F:	ECOD (20:10:01)
C		e3o6bC3	A: RuvA-C	X: post-HMGL domain-like	H: post-HMGL domain-like	T: Cobalamin_bind	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
F	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)
J	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)
H	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)
B	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)
A	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
E	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
E	1.10.238.200	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
G	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
I	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
C	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
C	1.10.238.200	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H, J	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
A, C, E, G, I	PF03556	Cullin binding (Cullin_binding)	Cullin binding	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J	Cell division control protein 53	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding nucleic acid binding DNA replication origin binding protein-macromolecule adaptor activity molecular adaptor activity ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding	regulation of mitotic cell cycle regulation of biological process regulation of cellular process biological regulation cellular process cell cycle regulation of cell cycle mitotic cell cycle organelle fusion cellular component organization organelle organization mitochondrial fusion cellular component organization or biogenesis mitochondrion organization regulation of mitotic cell cycle regulation of biological process regulation of cellular process biological regulation cellular process cell cycle regulation of cell cycle mitotic cell cycle organelle fusion cellular component organization organelle organization mitochondrial fusion cellular component organization or biogenesis mitochondrion organization cell division negative regulation of biological process cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process silent mating-type cassette heterochromatin formation negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process primary metabolic process protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal 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 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process subtelomeric heterochromatin formation RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by galactose regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription mitotic cell cycle process cell cycle phase transition G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle phase transition cell cycle process response to stimulus response to chemical cellular response to methylmercury response to methylmercury cellular response to stimulus DNA damage checkpoint signaling regulation of cell cycle phase transition signaling negative regulation of cell cycle intracellular signal transduction negative regulation of mitotic cell cycle cell communication mitotic DNA integrity checkpoint signaling cellular response to stress response to stress mitotic DNA damage checkpoint signaling negative regulation of cell cycle phase transition signal transduction mitotic intra-S DNA damage checkpoint signaling regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling DNA damage response signal transduction in response to DNA damage cell cycle G2/M phase transition G2/M transition of mitotic cell cycle regulation of localization hexose transmembrane transport regulation of transport transport positive regulation of biological process carbohydrate transport establishment of localization positive regulation of D-glucose transmembrane transport transmembrane transport localization regulation of transmembrane transport positive regulation of transport D-glucose transmembrane transport positive regulation of transmembrane transport regulation of D-glucose transmembrane transport monosaccharide transmembrane transport carbohydrate transmembrane transport positive regulation of cellular process	cellular anatomical structure intracellular anatomical structure cytoplasm cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle cellular anatomical structure intracellular anatomical structure cytoplasm cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region membrane-bounded organelle nucleus intracellular membrane-bounded organelle
A, C, E, G, I	Defective in cullin neddylation 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 protein-macromolecule adaptor activity molecular adaptor activity	primary metabolic process macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein neddylation protein modification by small protein conjugation protein modification by small protein conjugation or removal	protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J	IPR045093	Cullin	Family
B, D, F, H, J	IPR016158	Cullin homology domain	Domain
B, D, F, H, J	IPR016157	Cullin, conserved site	Conserved Site
B, D, F, H, J	IPR059120	Cullin-like, alpha+beta domain	Domain
B, D, F, H, J	IPR001373	Cullin, N-terminal	Domain
B, D, F, H, J	IPR019559	Cullin, neddylation domain	Domain
B, D, F, H, J	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B, D, F, H, J	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
B, D, F, H, J	IPR036317	Cullin homology domain superfamily	Homologous Superfamily
B, D, F, H, J	IPR016159	Cullin repeat-like-containing domain superfamily	Homologous Superfamily
A, C, E, G, I	IPR042460	DCN1-like, PONY binding domain	Homologous Superfamily
A, C, E, G, I	IPR054109	UBA-like domain	Domain
A, C, E, G, I	IPR009060	UBA-like superfamily	Homologous Superfamily
A, C, E, G, I	IPR005176	Potentiating neddylation domain	Domain
A, C, E, G, I	IPR014764	Defective-in-cullin neddylation protein	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.