4YII | pdb_00004yii

Structure of an APC2-UBCH10 complex reveals distinctive cullin-RING ligase mechanism for Anaphase-promoting complex/Cyclosome

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth U]	d4yiiu_	Alpha and beta proteins (a+b)	UBC-like	UBC-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth A]	SCOP2 Family	SCF complex WHB domain-like	8084655	4000322	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Winged helix DNA-binding domain	8084656	3000034	SCOP2 (2022-06-29)
A [auth U]	SCOP2B Superfamily	UBC-like	8033738	3000570	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)
B [auth A]	ANAPC2	e4yiiA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: ANAPC2	ECOD (1.6)
A [auth U]	UQ_con	e4yiiU1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	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 [auth U]	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A]	PF08672	Anaphase promoting complex (APC) subunit 2 (ANAPC2)	Anaphase promoting complex (APC) subunit 2	The anaphase promoting complex or cyclosome (APC2) is an E3 ubiquitin ligase which is part of the SCF family of ubiquitin ligases. Ubiquitin ligases catalyse the transfer of ubiquitin from the ubiquitin conjugating enzyme (E2), to the substrate prot ...	The anaphase promoting complex or cyclosome (APC2) is an E3 ubiquitin ligase which is part of the SCF family of ubiquitin ligases. Ubiquitin ligases catalyse the transfer of ubiquitin from the ubiquitin conjugating enzyme (E2), to the substrate protein.	Domain
A [auth U]	PF00179	Ubiquitin-conjugating enzyme (UQ_con)	Ubiquitin-conjugating enzyme	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cystein ...	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth A]	Anaphase-promoting complex subunit 2	ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	protein polyubiquitination protein branched polyubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process cellular 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 developmental process protein polyubiquitination protein branched polyubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process cellular 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 developmental process cellular developmental process cell differentiation multicellular organismal process regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization regulation of developmental process positive regulation of biological process cellular component organization positive regulation of developmental process multicellular organism development anatomical structure development regulation of synapse structure or activity synapse organization cellular component organization or biogenesis regulation of biological quality positive regulation of cellular process system development regulation of biological process biological regulation nervous system development developmental maturation synapse maturation regulation of synapse organization regulation of synapse maturation cell junction organization positive regulation of synapse maturation regulation of mitotic cell cycle cell cycle regulation of cell cycle mitotic cell cycle 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 anaphase-promoting complex-dependent catabolic process ubiquitin-dependent protein catabolic process cell division axon extension positive regulation of nervous system development regulation of growth axonogenesis regulation of cellular component size developmental growth cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development cell projection morphogenesis neuron differentiation neuron projection morphogenesis positive regulation of cell projection organization positive regulation of developmental growth regulation of cell projection organization positive regulation of cell development developmental growth involved in morphogenesis generation of neurons positive regulation of multicellular organismal process regulation of neuron projection development plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis regulation of axon extension regulation of nervous system development neurogenesis regulation of extent of cell growth positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process positive regulation of axon extension positive regulation of axonogenesis regulation of anatomical structure morphogenesis regulation of cell size neuron projection extension regulation of multicellular organismal development regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth growth positive regulation of cell growth axon development regulation of cell growth cell morphogenesis involved in neuron differentiation positive regulation of growth anatomical structure morphogenesis neuron development regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size regulation of synaptic plasticity trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission signaling cell-cell signaling chemical synaptic transmission cell communication positive regulation of synaptic plasticity synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication regulation of meiotic cell cycle sexual reproduction regulation of reproductive process reproductive process meiotic cell cycle regulation of chromosome segregation cell cycle phase transition chromosome segregation cell cycle process regulation of cell cycle process chromosome organization sister chromatid segregation regulation of chromosome organization regulation of organelle organization organelle organization mitotic cell cycle process regulation of sister chromatid segregation nuclear chromosome segregation metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition protein K11-linked ubiquitination protein K48-linked ubiquitination regulation of biosynthetic process negative regulation of metabolic process negative regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process regulation of macromolecule biosynthetic process regulation of metabolic process negative regulation of macromolecule metabolic process regulation of cell morphogenesis regulation of dendrite morphogenesis positive regulation of cell morphogenesis regulation of dendrite development dendrite development positive regulation of dendrite morphogenesis dendrite morphogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm 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 nuclear protein-containing complex transferase complex anaphase-promoting complex cullin-RING ubiquitin ligase complex nuclear ubiquitin ligase complex intracellular protein-containing complex
A [auth U]	Ubiquitin-conjugating enzyme E2 C	ubiquitin conjugating enzyme activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity binding adenyl ribonucleotide binding nucleotide binding ubiquitin conjugating enzyme activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein binding ubiquitin-like protein ligase binding enzyme binding	regulation of chromosome segregation regulation of cell cycle phase transition regulation of cellular process regulation of metaphase/anaphase transition of cell cycle regulation of cellular component organization cell cycle phase transition regulation of mitotic metaphase/anaphase transition mitotic cell cycle cellular component organization regulation of mitotic cell cycle cell cycle cellular component organization or biogenesis regulation of cell cycle chromosome segregation regulation of chromosome segregation regulation of cell cycle phase transition regulation of cellular process regulation of metaphase/anaphase transition of cell cycle regulation of cellular component organization cell cycle phase transition regulation of mitotic metaphase/anaphase transition mitotic cell cycle cellular component organization regulation of mitotic cell cycle cell cycle cellular component organization or biogenesis regulation of cell cycle chromosome segregation cell cycle process regulation of biological process regulation of cell cycle process biological regulation chromosome organization sister chromatid segregation regulation of chromosome organization regulation of organelle organization regulation of mitotic cell cycle phase transition organelle organization mitotic cell cycle process regulation of sister chromatid segregation nuclear chromosome segregation metaphase/anaphase transition of mitotic cell cycle cellular process metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition catabolic process proteolysis involved in protein catabolic process primary metabolic 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 anaphase-promoting complex-dependent catabolic process ubiquitin-dependent protein catabolic process metabolic process macromolecule metabolic process protein metabolic process positive regulation of organelle organization regulation of mitotic nuclear division positive regulation of mitotic nuclear division positive regulation of mitotic metaphase/anaphase transition positive regulation of mitotic cell cycle phase transition mitotic sister chromatid separation positive regulation of nuclear division regulation of chromosome separation regulation of mitotic sister chromatid separation positive regulation of cellular component organization positive regulation of biological process positive regulation of metaphase/anaphase transition of cell cycle mitotic sister chromatid segregation positive regulation of cell cycle process positive regulation of mitotic cell cycle positive regulation of cellular process mitotic nuclear division organelle fission positive regulation of cell cycle nuclear division chromosome separation positive regulation of cell cycle phase transition positive regulation of mitotic sister chromatid separation regulation of nuclear division positive regulation of chromosome separation cell division exit from mitosis positive regulation of exit from mitosis regulation of exit from mitosis protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal protein polymerization protein-containing complex organization homeostatic process free ubiquitin chain polymerization cellular component biogenesis cellular component assembly cellular homeostasis protein-containing complex assembly ubiquitin recycling regulation of protein modification process regulation of catalytic activity positive regulation of protein metabolic process regulation of protein ubiquitination regulation of transferase activity positive regulation of post-translational protein modification regulation of primary metabolic process regulation of ubiquitin protein ligase activity positive regulation of molecular function positive regulation of metabolic process positive regulation of ubiquitin protein ligase activity positive regulation of protein modification process positive regulation of macromolecule metabolic process regulation of ubiquitin-protein transferase activity regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification regulation of protein metabolic process positive regulation of catalytic activity regulation of macromolecule metabolic process positive regulation of ubiquitin-protein transferase activity regulation of molecular function regulation of metabolic process protein polyubiquitination protein K11-linked ubiquitination protein K48-linked ubiquitination	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane 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 nuclear protein-containing complex transferase complex anaphase-promoting complex cullin-RING ubiquitin ligase complex nuclear ubiquitin ligase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A]	IPR014786	Anaphase-promoting complex subunit 2, C-terminal	Domain
B [auth A]	IPR016158	Cullin homology domain	Domain
B [auth A]	IPR001373	Cullin, N-terminal	Domain
B [auth A]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B [auth A]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
B [auth A]	IPR036317	Cullin homology domain superfamily	Homologous Superfamily
B [auth A]	IPR044554	Anaphase-promoting complex subunit 2	Family
A [auth U]	IPR050113	Ubiquitin-conjugating enzyme	Family
A [auth U]	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
A [auth U]	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
A [auth U]	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth A]	Pharos: Q9UJX6	glioblastoma malignant ependymoma oligodendroglioma
A [auth U]	Pharos: O00762	breast carcinoma Chromosome Aberrations breast cancer malignant pancreatic neoplasm medulloblastoma pancreatic intraductal papillary-mucinous carcinoma psoriasis adrenal cortex carcinoma esophageal adenocarcinoma invasive ductal breast carcinoma lung cancer malignant mesothelioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm atopic eczema breast carcinoma Chromosome Aberrations breast cancer malignant pancreatic neoplasm medulloblastoma pancreatic intraductal papillary-mucinous carcinoma psoriasis adrenal cortex carcinoma esophageal adenocarcinoma invasive ductal breast carcinoma lung cancer malignant mesothelioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm atopic eczema ductal breast carcinoma in situ glioblastoma large cell medulloblastoma malignant ependymoma ovarian cancer primitive neuroectodermal tumor atypical teratoid rhabdoid tumor endometriosis hepatocellular carcinoma lung adenocarcinoma malignant glioma

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.