4ACO | pdb_00004aco

Structure of the budding yeast Ndc10 N-terminal domain

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Ndc10, DNA-binding domain-like	8046150	4004910	SCOP2 (2022-06-29)
A	SCOP2 Family	Ndc10, N-terminal domain-like	8053777	4007620	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNA breaking-rejoining enzymes	8053766	3001127	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	lambda integrase clamp domain-like	8053778	3000550	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		e4acoA1	A: Four-helical up-and-down bundle	X: N-terminal helical domain in restriction-modification system methylation subunit	H: N-terminal helical domain in restriction-modification system methylation subunit	T: HN	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.150.130	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	1.10.443.20	Mainly Alpha	Orthogonal Bundle	hpI Integrase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF16787	Centromere DNA-binding protein complex CBF3 subunit, domain 2 (NDC10_II)	Centromere DNA-binding protein complex CBF3 subunit, domain 2	NDC10_II is a the second of five domains on the Kluyveromyces lactis Ndc10 protein. Each subunit of the Ndc10 dimer binds a separate fragment of DNA, suggesting that Ndc10 stabilises a DNA loop at the centromere [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	CENTROMERE DNA-BINDING PROTEIN COMPLEX CBF3 SUBUNIT A	DNA binding binding nucleic acid binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding centromeric DNA binding DNA binding, bending	organelle assembly protein-containing complex organization chromosome organization membraneless organelle assembly cellular component organization cellular component biogenesis organelle organization cellular component assembly kinetochore assembly protein-containing complex assembly kinetochore organization cellular process cellular component organization or biogenesis cell cycle organelle assembly protein-containing complex organization chromosome organization membraneless organelle assembly cellular component organization cellular component biogenesis organelle organization cellular component assembly kinetochore assembly protein-containing complex assembly kinetochore organization cellular process cellular component organization or biogenesis cell cycle chromosome segregation cell cycle process mitotic spindle elongation spindle elongation microtubule cytoskeleton organization mitotic cell cycle mitotic sister chromatid segregation microtubule cytoskeleton organization involved in mitosis spindle organization mitotic nuclear division organelle fission sister chromatid segregation mitotic spindle organization nuclear division mitotic cell cycle process nuclear chromosome segregation microtubule-based process cytoskeleton organization septin ring organization septin ring assembly septin cytoskeleton organization	intracellular anatomical structure intracellular membraneless organelle chromosome chromosomal region kinetochore intracellular organelle cellular anatomical structure organelle membraneless organelle chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome cytoskeleton intracellular anatomical structure intracellular membraneless organelle chromosome chromosomal region kinetochore intracellular organelle cellular anatomical structure organelle membraneless organelle chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome cytoskeleton spindle spindle midzone microtubule cytoskeleton microtubule organizing center spindle pole body membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex CBF3 complex intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR022210	Transcription activator GCR1-like domain	Domain
A	IPR049055	NDC10, N-terminal domain	Domain
A	IPR010998	Integrase/recombinase, N-terminal	Homologous Superfamily
A	IPR038279	Ndc10, domain 2 superfamily	Homologous Superfamily
A	IPR031872	Ndc10, domain 2	Domain

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.