2QYF | pdb_00002qyf

Crystal structure of the Mad2/p31(comet)/Mad2-binding peptide ternary complex

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)
C	d2qyfc_	Alpha and beta proteins (a+b)	The spindle assembly checkpoint protein mad2	The spindle assembly checkpoint protein mad2	The spindle assembly checkpoint protein mad2	The spindle assembly checkpoint protein mad2	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2qyfa_	Alpha and beta proteins (a+b)	The spindle assembly checkpoint protein mad2	The spindle assembly checkpoint protein mad2	The spindle assembly checkpoint protein mad2	The spindle assembly checkpoint protein mad2	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)
D	SCOP2 Family	p31comet-like	8004012	4000364	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	HORMA/p31comet-like	8004013	3000150	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	HORMA/p31comet-like	8004013	3000150	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	HORMA/p31comet-like	8004003	3000150	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HORMA/p31comet-like	8004003	3000150	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	DUF3239	e2qyfD1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: DUF3239	ECOD (develop294)
B	p31comet	e2qyfB1	A: alpha bundles	X: The spindle assembly checkpoint protein mad2	H: The spindle assembly checkpoint protein mad2	T: The spindle assembly checkpoint protein mad2	F: p31comet	ECOD (develop294)
C	DUF3239	e2qyfC1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: DUF3239	ECOD (develop294)
A	DUF3239	e2qyfA1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: DUF3239	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.900.20	Alpha Beta	2-Layer Sandwich	Cell Cycle, Spindle Assembly Checkpoint Protein	Chain A	CATH (4.3.0)
B	3.30.900.20	Alpha Beta	2-Layer Sandwich	Cell Cycle, Spindle Assembly Checkpoint Protein	Chain A	CATH (4.3.0)
C	3.30.900.10	Alpha Beta	2-Layer Sandwich	Cell Cycle, Spindle Assembly Checkpoint Protein	Chain A	CATH (4.3.0)
A	3.30.900.10	Alpha Beta	2-Layer Sandwich	Cell Cycle, Spindle Assembly Checkpoint Protein	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF02301	HORMA domain (HORMA)	HORMA domain	The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognise chromatin states that result from DNA adducts, double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. MAD2 is a spindle ...	The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognise chromatin states that result from DNA adducts, double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F	peptide	-	-	-
B, D	MAD2L1-binding protein	-	cellular response to stimulus positive regulation of organelle organization negative regulation of spindle checkpoint response to stimulus spindle checkpoint signaling regulation of signal transduction regulation of mitotic nuclear division negative regulation of mitotic spindle assembly checkpoint signaling intracellular signal transduction negative regulation of mitotic cell cycle regulation of cell cycle checkpoint negative regulation of mitotic sister chromatid segregation negative regulation of chromosome organization positive regulation of mitotic metaphase/anaphase transition positive regulation of mitotic cell cycle phase transition cellular response to stimulus positive regulation of organelle organization negative regulation of spindle checkpoint response to stimulus spindle checkpoint signaling regulation of signal transduction regulation of mitotic nuclear division negative regulation of mitotic spindle assembly checkpoint signaling intracellular signal transduction negative regulation of mitotic cell cycle regulation of cell cycle checkpoint negative regulation of mitotic sister chromatid segregation negative regulation of chromosome organization positive regulation of mitotic metaphase/anaphase transition positive regulation of mitotic cell cycle phase transition negative regulation of cell cycle phase transition mitotic spindle checkpoint signaling mitotic sister chromatid separation negative regulation of sister chromatid segregation mitotic spindle assembly checkpoint signaling sister chromatid segregation regulation of mitotic sister chromatid segregation deactivation of mitotic spindle assembly checkpoint regulation of response to stimulus negative regulation of mitotic nuclear division regulation of chromosome segregation regulation of cellular component organization regulation of mitotic sister chromatid separation positive regulation of cellular component organization spindle assembly checkpoint signaling negative regulation of intracellular signal transduction regulation of mitotic metaphase/anaphase transition mitotic cell cycle regulation of mitotic cell cycle mitotic sister chromatid segregation positive regulation of metaphase/anaphase transition of cell cycle positive regulation of cell cycle process negative regulation of mitotic metaphase/anaphase transition positive regulation of mitotic cell cycle regulation of cell cycle negative regulation of chromosome separation positive regulation of cellular process cell cycle process mitotic nuclear division regulation of signaling chromosome organization negative regulation of signal transduction positive regulation of cell cycle cell cycle checkpoint signaling negative regulation of chromosome segregation negative regulation of nuclear division chromosome separation positive regulation of cell cycle phase transition negative regulation of metaphase/anaphase transition of cell cycle nuclear chromosome segregation regulation of cell communication cellular process regulation of cellular process regulation of cell cycle phase transition negative regulation of biological process negative regulation of cell cycle positive regulation of mitotic nuclear division cell communication signal transduction cell cycle chromosome segregation regulation of biological process negative regulation of cellular component organization regulation of cell cycle process regulation of spindle checkpoint positive regulation of nuclear division regulation of chromosome organization regulation of organelle organization regulation of mitotic cell cycle phase transition positive regulation of chromosome organization mitotic cell cycle process regulation of chromosome separation negative regulation of cell cycle checkpoint regulation of metaphase/anaphase transition of cell cycle regulation of mitotic spindle checkpoint signaling negative regulation of signaling regulation of mitotic cell cycle spindle assembly checkpoint positive regulation of biological process cell cycle phase transition negative regulation of cell communication cellular component organization regulation of intracellular signal transduction negative regulation of cellular process cellular component organization or biogenesis positive regulation of chromosome segregation negative regulation of mitotic cell cycle phase transition negative regulation of response to stimulus organelle fission biological regulation negative regulation of cell cycle process positive regulation of mitotic sister chromatid segregation mitotic cell cycle checkpoint signaling organelle organization nuclear division negative regulation of organelle organization regulation of sister chromatid segregation negative regulation of mitotic sister chromatid separation regulation of nuclear division positive regulation of mitotic sister chromatid separation metaphase/anaphase transition of mitotic cell cycle positive regulation of chromosome separation metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition exit from mitosis regulation of exit from mitosis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoskeleton spindle microtubule cytoskeleton cytoplasm nuclear membrane membrane endomembrane system organelle envelope nuclear envelope organelle membrane nucleoplasm
A, C	Mitotic spindle assembly checkpoint protein MAD2A	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity	cellular process cell division cellular response to stimulus positive regulation of cell communication regulation of cellular process regulation of cell cycle phase transition positive regulation of signal transduction response to stimulus positive regulation of cell cycle checkpoint negative regulation of biological process spindle checkpoint signaling negative regulation of cell cycle regulation of signal transduction regulation of mitotic nuclear division cellular process cell division cellular response to stimulus positive regulation of cell communication regulation of cellular process regulation of cell cycle phase transition positive regulation of signal transduction response to stimulus positive regulation of cell cycle checkpoint negative regulation of biological process spindle checkpoint signaling negative regulation of cell cycle regulation of signal transduction regulation of mitotic nuclear division intracellular signal transduction negative regulation of mitotic cell cycle cell communication regulation of cell cycle checkpoint negative regulation of mitotic sister chromatid segregation negative regulation of chromosome organization negative regulation of cell cycle phase transition mitotic spindle checkpoint signaling signal transduction cell cycle mitotic sister chromatid separation chromosome segregation negative regulation of sister chromatid segregation mitotic spindle assembly checkpoint signaling regulation of biological process negative regulation of cellular component organization regulation of cell cycle process regulation of spindle checkpoint sister chromatid segregation positive regulation of intracellular signal transduction regulation of chromosome organization regulation of organelle organization regulation of mitotic cell cycle phase transition regulation of mitotic sister chromatid segregation mitotic cell cycle process regulation of response to stimulus positive regulation of mitotic cell cycle spindle assembly checkpoint regulation of chromosome separation negative regulation of mitotic nuclear division regulation of chromosome segregation regulation of cellular component organization regulation of mitotic sister chromatid separation regulation of metaphase/anaphase transition of cell cycle regulation of mitotic spindle checkpoint signaling regulation of mitotic cell cycle spindle assembly checkpoint spindle assembly checkpoint signaling positive regulation of biological process cell cycle phase transition regulation of mitotic metaphase/anaphase transition mitotic cell cycle cellular component organization positive regulation of response to stimulus regulation of mitotic cell cycle regulation of intracellular signal transduction negative regulation of cellular process mitotic sister chromatid segregation positive regulation of cell cycle process negative regulation of mitotic metaphase/anaphase transition cellular component organization or biogenesis regulation of cell cycle negative regulation of chromosome separation positive regulation of cellular process cell cycle process positive regulation of spindle checkpoint mitotic nuclear division regulation of signaling negative regulation of mitotic cell cycle phase transition organelle fission biological regulation chromosome organization negative regulation of cell cycle process positive regulation of cell cycle cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling organelle organization nuclear division negative regulation of chromosome segregation negative regulation of nuclear division negative regulation of organelle organization chromosome separation regulation of sister chromatid segregation negative regulation of mitotic sister chromatid separation regulation of nuclear division negative regulation of metaphase/anaphase transition of cell cycle nuclear chromosome segregation metaphase/anaphase transition of mitotic cell cycle regulation of cell communication metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition positive regulation of signaling catabolic process macromolecule catabolic process negative regulation of protein catabolic process regulation of primary metabolic process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process regulation of protein metabolic process negative regulation of metabolic process primary metabolic process protein catabolic process regulation of macromolecule metabolic process regulation of catabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process negative regulation of post-translational protein modification negative regulation of ubiquitin protein ligase activity regulation of protein modification process regulation of catalytic activity negative regulation of catalytic activity regulation of protein ubiquitination regulation of transferase activity regulation of ubiquitin protein ligase activity negative regulation of ubiquitin-protein transferase activity protein ubiquitination negative regulation of protein modification process regulation of ubiquitin-protein transferase activity negative regulation of protein ubiquitination regulation of protein modification by small protein conjugation or removal protein modification process negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification negative regulation of molecular function regulation of molecular function macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton chromosome chromosomal region kinetochore chromosome, centromeric region intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton chromosome chromosomal region kinetochore chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome cytoplasm cytosol perinuclear region of cytoplasm membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex mitotic checkpoint complex intracellular membrane-bounded organelle mitotic spindle assembly checkpoint MAD1-MAD2 complex mitotic spindle membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen endomembrane system organelle envelope nuclear envelope nuclear pore nuclear basket nuclear pore

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR053729	MAD2L1-binding domain-containing protein	Homologous Superfamily
B, D	IPR009511	Mad1/Cdc20-bound-Mad2 binding protein	Family
A, C	IPR045091	Mad2-like	Family
A, C	IPR036570	HORMA domain superfamily	Homologous Superfamily
A, C	IPR003511	HORMA domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: Q15013	acute myeloid leukemia Sjogren syndrome medulloblastoma ovarian cancer
A, C	Pharos: Q13257	polycystic ovary syndrome esophageal squamous cell carcinoma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor adrenal cortex carcinoma Sjogren syndrome breast cancer ductal breast carcinoma in situ glioblastoma IgA glomerulonephritis lung adenocarcinoma malignant ependymoma medulloblastoma polycystic ovary syndrome esophageal squamous cell carcinoma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor adrenal cortex carcinoma Sjogren syndrome breast cancer ductal breast carcinoma in situ glioblastoma IgA glomerulonephritis lung adenocarcinoma malignant ependymoma medulloblastoma ovarian cancer pituitary cancer psoriasis atopic eczema breast carcinoma endometriosis heart disease invasive ductal breast carcinoma lung cancer malignant glioma nasopharyngeal carcinoma pancreatic intraductal papillary-mucinous carcinoma Sclerocystic Ovaries atypical teratoid rhabdoid tumor Crohn disease hepatocellular carcinoma large cell medulloblastoma malignant colon neoplasm

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.