2VE7 | pdb_00002ve7

Crystal structure of a bonsai version of the human Ndc80 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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Calponin-homology domain, CH-domain	8051976	3000264	SCOP2B (2022-06-29)
B	SCOP2 Family	Ndc80/Hec family	8018821	4004024	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Calponin-homology domain, CH-domain	8051976	3000264	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Calponin-homology domain, CH-domain	8053595	3000264	SCOP2B (2022-06-29)
D	SCOP2 Family	Nuf2-like	8044873	4004186	SCOP2 (2022-06-29)
D	SCOP2 Family	Spc25-like	8053598	4003402	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Calponin-homology domain, CH-domain	8053595	3000264	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	RWD domain-like	8053599	3000774	SCOP2 (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		e2ve7A1	A: Single-stranded left-handed beta-helix	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: DNA_topoisoIV	F:	ECOD (20:10:01)
B		e2ve7B1	A: Anticodon-binding domain of Class II aaRS	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: HGTP_anticodon	F:	ECOD (20:10:01)
C		e2ve7C3	A: DEATH domain	X: 6-phosphogluconate dehydrogenase C-terminal domain-like	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: Cupin_2	F:	ECOD (20:10:01)
D		e2ve7D1	A: Kringle-like	X: Kringle-like	H: Kringle-like	T: FliT	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.418.30	Mainly Alpha	Orthogonal Bundle	Actin-binding Protein, T-fimbrin	domain 1	CATH (4.3.0)
A	6.10.250.1950	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	1.10.418.30	Mainly Alpha	Orthogonal Bundle	Actin-binding Protein, T-fimbrin	domain 1	CATH (4.3.0)
C	1.10.418.60	Mainly Alpha	Orthogonal Bundle	Actin-binding Protein, T-fimbrin	domain 1	CATH (4.3.0)
C	3.30.160.570	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Ncd80 complex, Spc24 subunit	CATH (4.3.0)
D	1.10.418.60	Mainly Alpha	Orthogonal Bundle	Actin-binding Protein, T-fimbrin	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF08234	Chromosome segregation protein Spc25 (Spindle_Spc25)	Chromosome segregation protein Spc25	-	Family
A, B	PF18077	Domain of unknown function (DUF5595) (DUF5595)	Domain of unknown function (DUF5595)	This domain is found in Nude C 80 (Ndc80) proteins which can be found in species such as Homo sapiens. Ndc80 protein complexes are a core component of the end-on attachment sites for kinetochore microtubules. Ndc80 is also known as Hec1, for highly e ...	This domain is found in Nude C 80 (Ndc80) proteins which can be found in species such as Homo sapiens. Ndc80 protein complexes are a core component of the end-on attachment sites for kinetochore microtubules. Ndc80 is also known as Hec1, for highly expressed in cancer 1 [1].	Domain
A, B	PF03801	HEC/Ndc80p family (Ndc80_HEC)	HEC/Ndc80p family	-	Family
C, D	PF08286	Spc24 subunit of Ndc80 (Spc24)	Spc24 subunit of Ndc80	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	KINETOCHORE PROTEIN HEC1, KINETOCHORE PROTEIN SPC25	protein binding binding cyclin binding cytoskeletal protein binding microtubule binding tubulin binding protein-macromolecule adaptor activity molecular adaptor activity kinetochore adaptor activity identical protein binding	cellular process cell cycle mitotic cell cycle metaphase chromosome alignment localization attachment of spindle microtubules to kinetochore chromosome localization organelle localization nuclear chromosome segregation chromosome segregation cell cycle process cell cycle G2/M phase transition sexual reproduction reproductive process cellular process cell cycle mitotic cell cycle metaphase chromosome alignment localization attachment of spindle microtubules to kinetochore chromosome localization organelle localization nuclear chromosome segregation chromosome segregation cell cycle process cell cycle G2/M phase transition sexual reproduction reproductive process meiotic cell cycle cell cycle phase transition meiotic cell cycle process meiotic cell cycle phase transition meiosis I cell cycle process G2/MI transition of meiotic cell cycle mitotic metaphase chromosome alignment cellular component organization mitotic sister chromatid segregation cellular component organization or biogenesis mitotic nuclear division organelle fission attachment of mitotic spindle microtubules to kinetochore chromosome organization sister chromatid segregation organelle organization nuclear division mitotic cell cycle 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 mitotic sister chromatid separation 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 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 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 regulation of mitotic metaphase/anaphase transition positive regulation of response to stimulus regulation of mitotic cell cycle regulation of intracellular signal transduction negative regulation of cellular process positive regulation of cell cycle process negative regulation of mitotic metaphase/anaphase transition regulation of cell cycle negative regulation of chromosome separation positive regulation of cellular process positive regulation of spindle checkpoint regulation of signaling negative regulation of mitotic cell cycle phase transition biological regulation negative regulation of cell cycle process positive regulation of cell cycle cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling 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 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 microtubule organizing center organization microtubule cytoskeleton organization centrosome duplication centrosome cycle microtubule-based process cytoskeleton organization meiotic chromosome segregation membraneless organelle assembly female gamete generation gamete generation cellular component biogenesis cellular component assembly meiosis I female meiotic nuclear division spindle assembly involved in female meiosis I meiotic nuclear division spindle organization organelle assembly multicellular organismal reproductive process meiotic spindle organization meiotic spindle assembly spindle assembly female meiosis I spindle assembly involved in female meiosis kinetochore organization regulation of protein stability regulation of biological quality establishment of organelle localization cellular localization spindle localization establishment or maintenance of cell polarity establishment of mitotic spindle localization establishment of spindle localization establishment of spindle orientation establishment of localization in cell microtubule cytoskeleton organization involved in mitosis establishment of localization establishment of cell polarity establishment of mitotic spindle orientation mitotic spindle organization cell population proliferation muscle cell proliferation skeletal muscle satellite cell proliferation skeletal muscle cell proliferation striated muscle cell proliferation	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body nucleoplasm cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton cytoplasm cytosol Ndc80 complex protein-containing complex chromosome chromosomal region kinetochore chromosome, centromeric region outer kinetochore condensed chromosome, centromeric region condensed chromosome
C, D	KINETOCHORE PROTEIN NUF2, KINETOCHORE PROTEIN SPC24	cytoskeletal protein binding microtubule binding protein binding binding tubulin binding protein-containing complex binding	cellular response to stimulus regulation of cellular process regulation of cell cycle phase transition response to stimulus negative regulation of biological process spindle checkpoint signaling negative regulation of cell cycle regulation of mitotic nuclear division intracellular signal transduction negative regulation of mitotic cell cycle cell communication negative regulation of mitotic sister chromatid segregation negative regulation of chromosome organization negative regulation of cell cycle phase transition cellular response to stimulus regulation of cellular process regulation of cell cycle phase transition response to stimulus negative regulation of biological process spindle checkpoint signaling negative regulation of cell cycle regulation of mitotic nuclear division intracellular signal transduction negative regulation of mitotic cell cycle cell communication 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 sister chromatid segregation 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 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 signaling spindle assembly checkpoint signaling cell cycle phase transition regulation of mitotic metaphase/anaphase transition mitotic cell cycle cellular component organization regulation of mitotic cell cycle negative regulation of cellular process mitotic sister chromatid segregation negative regulation of mitotic metaphase/anaphase transition cellular component organization or biogenesis regulation of cell cycle negative regulation of chromosome separation cell cycle process mitotic nuclear division negative regulation of mitotic cell cycle phase transition organelle fission biological regulation chromosome organization negative regulation of cell cycle process 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 cellular process metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition metaphase chromosome alignment localization attachment of spindle microtubules to kinetochore chromosome localization organelle localization cell division mitotic metaphase chromosome alignment attachment of mitotic spindle microtubules to kinetochore microtubule cytoskeleton organization mitotic spindle organization microtubule-based process cytoskeleton organization microtubule cytoskeleton organization involved in mitosis spindle organization meiotic chromosome segregation sexual reproduction reproductive process meiotic cell cycle meiotic cell cycle process meiotic nuclear division kinetochore organization	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol Ndc80 complex protein-containing complex intracellular membraneless organelle chromosome chromosomal region kinetochore intracellular organelle organelle membraneless organelle chromosome, centromeric region cellular anatomical structure intracellular anatomical structure cytoplasm cytosol Ndc80 complex protein-containing complex intracellular membraneless organelle chromosome chromosomal region kinetochore intracellular organelle organelle membraneless organelle chromosome, centromeric region outer kinetochore condensed chromosome, centromeric region supramolecular complex condensed chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen organelle lumen nuclear lumen nucleoplasm membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR040967	Domain of unknown function DUF5595	Domain
A, B	IPR057091	Kinetochore protein NDC80 loop region	Domain
A, B	IPR005550	Kinetochore protein Ndc80	Family
A, B	IPR055260	Kinetochore protein Ndc80, CH domain	Domain
A, B	IPR038273	Ndc80 domain superfamily	Homologous Superfamily
A, B	IPR045143	Kinetochore protein Spc25	Family
A, B	IPR013255	Chromosome segregation protein Spc25, C-terminal	Domain
C, D	IPR013252	Kinetochore-Ndc80 subunit Spc24	Family
C, D	IPR038275	Nuf2, N-terminal domain superfamily	Homologous Superfamily
C, D	IPR005549	Kinetochore protein Nuf2, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9HBM1	malignant mesothelioma nasopharyngeal carcinoma ovarian cancer pilocytic astrocytoma adrenal cortex carcinoma Sjogren syndrome atypical teratoid rhabdoid tumor cholangiocarcinoma glioblastoma interstitial cystitis lung adenocarcinoma malignant ependymoma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma malignant mesothelioma nasopharyngeal carcinoma ovarian cancer pilocytic astrocytoma adrenal cortex carcinoma Sjogren syndrome atypical teratoid rhabdoid tumor cholangiocarcinoma glioblastoma interstitial cystitis lung adenocarcinoma malignant ependymoma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor astrocytic tumor ulcerative colitis breast cancer ductal breast carcinoma in situ hepatocellular carcinoma invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm psoriasis atopic eczema breast carcinoma endometriosis IgA glomerulonephritis large cell medulloblastoma malignant colon neoplasm metabolic syndrome X pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor adrenal cortex carcinoma breast cancer endometriosis IgA glomerulonephritis lung adenocarcinoma malignant colon neoplasm malignant mesothelioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm psoriasis atopic eczema breast carcinoma glioblastoma invasive ductal breast carcinoma lung cancer malignant ependymoma medulloblastoma ovarian cancer pilocytic astrocytoma ulcerative colitis atypical teratoid rhabdoid tumor ductal breast carcinoma in situ hepatocellular carcinoma large cell medulloblastoma lung carcinoma malignant glioma
C, D	Pharos: Q9BZD4	abdominal aortic aneurysm heart disease myocardial infarction peripheral arterial disease breast cancer large cell medulloblastoma osteosarcoma primitive neuroectodermal tumor carotid artery disease medulloblastoma ovarian cancer psoriasis oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor abdominal aortic aneurysm heart disease myocardial infarction peripheral arterial disease breast cancer large cell medulloblastoma osteosarcoma primitive neuroectodermal tumor carotid artery disease medulloblastoma ovarian cancer psoriasis oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor adrenal cortex carcinoma atypical teratoid rhabdoid tumor Crohn disease glioblastoma large cell medulloblastoma malignant glioma nasopharyngeal carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis astrocytic tumor breast cancer ductal breast carcinoma in situ hepatocellular carcinoma lung adenocarcinoma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma ulcerative colitis atopic eczema breast carcinoma endometriosis invasive ductal breast carcinoma malignant ependymoma medulloblastoma

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.