3HYM | pdb_00003hym

Insights into Anaphase Promoting Complex TPR subdomain assembly from a CDC26-APC6 structure

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
K	SCOP2B Superfamily	CDC26-like	8053843	3002235	SCOP2B (2022-06-29)
I	SCOP2 Family	ANAPC_CDC26-like	8044943	4004216	SCOP2 (2022-06-29)
I	SCOP2 Superfamily	CDC26-like	8053843	3002235	SCOP2 (2022-06-29)
G	SCOP2B Superfamily	CDC26-like	8053843	3002235	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	CDC26-like	8053843	3002235	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CDC26-like	8053843	3002235	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CDC26-like	8053843	3002235	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)
L	TPR_1, TPR_7, TPR_12	e3hymL4	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: TPR_1, TPR_7, TPR_12	ECOD (v294.1)
J	TPR_1, TPR_7, TPR_12	e3hymJ4	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: TPR_1, TPR_7, TPR_12	ECOD (v294.1)
H	TPR_1, TPR_7, TPR_12	e3hymH4	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: TPR_1, TPR_7, TPR_12	ECOD (v294.1)
F	TPR_1, TPR_7, TPR_12	e3hymF4	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: TPR_1, TPR_7, TPR_12	ECOD (v294.1)
D	TPR_8, PF31234	e3hymD4	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: TPR_8, PF31234	ECOD (v294.1)
B		e3hymB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	1.25.40.10	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Tetratricopeptide repeat domain	CATH (4.3.0)
J	1.25.40.10	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Tetratricopeptide repeat domain	CATH (4.3.0)
H	1.25.40.10	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Tetratricopeptide repeat domain	CATH (4.3.0)
F	1.25.40.10	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Tetratricopeptide repeat domain	CATH (4.3.0)
D	1.25.40.10	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Tetratricopeptide repeat domain	CATH (4.3.0)
B	1.25.40.10	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Tetratricopeptide repeat domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K	PF10471	Anaphase-promoting complex APC subunit CDC26 (ANAPC_CDC26)	Anaphase-promoting complex APC subunit CDC26	-	Family
B, D, F, H, J B, D, F, H, J, L	PF13424	Tetratricopeptide repeat (TPR_12)	Tetratricopeptide repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G, I A, C, E, G, I, K	Anaphase-promoting complex subunit CDC26	-	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 regulation of mitotic cell cycle 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 regulation of mitotic cell cycle regulation of biological process regulation of cellular process biological regulation cell cycle regulation of cell cycle mitotic cell cycle 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 anaphase-promoting complex-dependent catabolic process ubiquitin-dependent protein catabolic process protein K11-linked ubiquitination protein K48-linked ubiquitination regulation of meiotic cell cycle sexual reproduction regulation of reproductive process reproductive process meiotic cell cycle cell division	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
B, D, F, H, J B, D, F, H, J, L	Cell division cycle protein 16 homolog	-	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 regulation of mitotic cell cycle 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 regulation of mitotic cell cycle regulation of biological process regulation of cellular process biological regulation cell cycle regulation of cell cycle mitotic cell cycle 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 anaphase-promoting complex-dependent catabolic process ubiquitin-dependent protein catabolic process positive regulation of organelle organization regulation of cell cycle phase transition 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 chromosome segregation regulation of cell cycle process positive regulation of nuclear division sister chromatid segregation regulation of chromosome organization regulation of organelle organization regulation of mitotic cell cycle phase transition mitotic cell cycle process regulation of chromosome separation regulation of chromosome segregation regulation of metaphase/anaphase transition of cell cycle regulation of cellular component organization regulation of mitotic sister chromatid separation positive regulation of cellular component organization positive regulation of biological process cell cycle phase transition regulation of mitotic metaphase/anaphase transition cellular component organization 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 cellular component organization or biogenesis positive regulation of cellular process cell cycle process mitotic nuclear division organelle fission chromosome organization positive regulation of cell cycle organelle organization nuclear division chromosome separation regulation of sister chromatid segregation positive regulation of cell cycle phase transition positive regulation of mitotic sister chromatid separation regulation of nuclear division nuclear chromosome segregation metaphase/anaphase transition of mitotic cell cycle positive regulation of chromosome separation metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition protein K11-linked ubiquitination protein K48-linked ubiquitination cell division regulation of meiotic cell cycle sexual reproduction regulation of reproductive process reproductive process meiotic cell cycle	intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton membrane-bounded organelle protein-containing complex ubiquitin ligase complex catalytic complex intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton membrane-bounded organelle protein-containing complex ubiquitin ligase complex catalytic complex nucleus nuclear protein-containing complex transferase complex intracellular membrane-bounded organelle anaphase-promoting complex cullin-RING ubiquitin ligase complex nuclear ubiquitin ligase complex intracellular protein-containing complex cytoplasm cytosol mitotic spindle spindle membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K	IPR018860	Anaphase-promoting complex, subunit CDC26	Family
B, D, F, H, J B, D, F, H, J, L	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR019734	Tetratricopeptide repeat	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G, I A, C, E, G, I, K	Pharos: Q8NHZ8	diabetes mellitus
B, D, F, H, J B, D, F, H, J, L	Pharos: Q13042	lymphoplasmacytic lymphoma nodular sclerosis classical Hodgkin lymphoma pancreatic ductal adenocarcinoma malignant colon neoplasm osteosarcoma Pick disease medulloblastoma ovarian cancer

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.