2VE7

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	Ndc80_HEC	e2ve7A1	A: alpha bundles	X: CH domain-like	H: Calponin-homology domain-like (From Topology)	T: Calponin-homology domain-like	F: Ndc80_HEC	ECOD (1.6)
A	Spindle_Spc25	e2ve7A3	A: a+b two layers	X: Kinetochore globular domain-like (From Topology)	H: Kinetochore globular domain-like (From Topology)	T: Kinetochore globular domain-like	F: Spindle_Spc25	ECOD (1.6)
A	KOG0995	e2ve7A2	A: extended segments	X: Helical hairpin in Ndc80 (From Topology)	H: Helical hairpin in Ndc80 (From Topology)	T: Helical hairpin in Ndc80	F: KOG0995	ECOD (1.6)
B	Ndc80_HEC	e2ve7B1	A: alpha bundles	X: CH domain-like	H: Calponin-homology domain-like (From Topology)	T: Calponin-homology domain-like	F: Ndc80_HEC	ECOD (1.6)
B	Spindle_Spc25	e2ve7B3	A: a+b two layers	X: Kinetochore globular domain-like (From Topology)	H: Kinetochore globular domain-like (From Topology)	T: Kinetochore globular domain-like	F: Spindle_Spc25	ECOD (1.6)
B	KOG0995	e2ve7B2	A: extended segments	X: Helical hairpin in Ndc80 (From Topology)	H: Helical hairpin in Ndc80 (From Topology)	T: Helical hairpin in Ndc80	F: KOG0995	ECOD (1.6)
C	Nuf2	e2ve7C4	A: alpha bundles	X: CH domain-like	H: Calponin-homology domain-like (From Topology)	T: Calponin-homology domain-like	F: Nuf2	ECOD (1.6)
C	Spc24	e2ve7C3	A: a+b two layers	X: Kinetochore globular domain-like (From Topology)	H: Kinetochore globular domain-like (From Topology)	T: Kinetochore globular domain-like	F: Spc24	ECOD (1.6)
D	Nuf2	e2ve7D1	A: alpha bundles	X: CH domain-like	H: Calponin-homology domain-like (From Topology)	T: Calponin-homology domain-like	F: Nuf2	ECOD (1.6)
D	Spc24	e2ve7D2	A: a+b two layers	X: Kinetochore globular domain-like (From Topology)	H: Kinetochore globular domain-like (From Topology)	T: Kinetochore globular domain-like	F: Spc24	ECOD (1.6)

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
C, D	PF03800	Nuf2 family (Nuf2)	Nuf2 family	-	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	microtubule cytoskeleton organization mitotic cell cycle mitotic spindle organization cellular component organization organelle organization mitotic cell cycle process cellular process microtubule-based process cell cycle cellular component organization or biogenesis cytoskeleton organization microtubule cytoskeleton organization involved in mitosis spindle organization cell cycle process microtubule cytoskeleton organization mitotic cell cycle mitotic spindle organization cellular component organization organelle organization mitotic cell cycle process cellular process microtubule-based process cell cycle cellular component organization or biogenesis cytoskeleton organization microtubule cytoskeleton organization involved in mitosis spindle organization cell cycle process 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 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 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 regulation of mitotic cell cycle negative regulation of cellular process mitotic sister chromatid segregation negative regulation of mitotic metaphase/anaphase transition regulation of cell cycle negative regulation of chromosome separation 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 nuclear division negative regulation of chromosome segregation chromosome separation negative regulation of organelle organization negative regulation of nuclear division 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 metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition establishment of organelle localization cellular localization attachment of spindle microtubules to kinetochore establishment of localization metaphase chromosome alignment localization chromosome localization organelle localization establishment of localization in cell establishment of chromosome localization cell division cell cycle G2/M phase transition sexual reproduction reproductive process meiotic cell cycle 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 attachment of mitotic spindle microtubules to kinetochore positive regulation of cell communication positive regulation of signal transduction positive regulation of cell cycle checkpoint regulation of signal transduction regulation of cell cycle checkpoint regulation of spindle checkpoint positive regulation of intracellular signal transduction regulation of response to stimulus positive regulation of mitotic cell cycle spindle assembly checkpoint regulation of mitotic spindle checkpoint regulation of mitotic cell cycle spindle assembly checkpoint positive regulation of biological process positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of cell cycle process positive regulation of cellular process positive regulation of spindle checkpoint regulation of signaling positive regulation of cell cycle regulation of cell communication positive regulation of signaling microtubule organizing center organization centrosome duplication centrosome cycle meiotic chromosome segregation non-membrane-bounded 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 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 spindle localization establishment or maintenance of cell polarity establishment of mitotic spindle localization establishment of spindle localization establishment of spindle orientation establishment of cell polarity establishment of mitotic spindle orientation cell population proliferation muscle cell proliferation skeletal muscle satellite cell proliferation skeletal muscle cell proliferation striated muscle cell proliferation	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol Ndc80 complex protein-containing complex chromosome chromosomal region kinetochore intracellular organelle organelle intracellular non-membrane-bounded organelle chromosome, centromeric region outer kinetochore intracellular anatomical structure cytoplasm cellular anatomical entity cytosol Ndc80 complex protein-containing complex chromosome chromosomal region kinetochore intracellular organelle organelle intracellular non-membrane-bounded organelle chromosome, centromeric region outer kinetochore condensed chromosome, centromeric region supramolecular complex condensed chromosome non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle membrane centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
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 chromosome separation negative regulation of organelle organization negative regulation of nuclear division 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 establishment of organelle localization cellular localization attachment of spindle microtubules to kinetochore establishment of localization metaphase chromosome alignment localization chromosome localization organelle localization establishment of localization in cell establishment of chromosome 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	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol Ndc80 complex protein-containing complex chromosome chromosomal region kinetochore intracellular organelle organelle intracellular non-membrane-bounded organelle chromosome, centromeric region outer kinetochore intracellular anatomical structure cytoplasm cellular anatomical entity cytosol Ndc80 complex protein-containing complex chromosome chromosomal region kinetochore intracellular organelle organelle intracellular non-membrane-bounded organelle chromosome, centromeric region outer kinetochore condensed chromosome, centromeric region supramolecular complex condensed chromosome non-membrane-bounded organelle 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	IPR045143	Kinetochore protein Spc25	Family
A, B	IPR013255	Chromosome segregation protein Spc25, C-terminal	Domain
A, B	IPR040967	Domain of unknown function DUF5595	Domain
A, B	IPR005550	Kinetochore protein Ndc80	Family
A, B	IPR038273	Ndc80 domain superfamily	Homologous Superfamily
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: O14777	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 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 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
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 National Science Foundation (DBI-1832184), 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 R01GM133198.