6GYS | pdb_00006gys

Cryo-EM structure of the CBF3-CEN3 complex of the budding yeast kinetochore

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
B	SCOP2B Superfamily	Cep3/Upc2 domain-like	8093129	3002679	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ARM repeat-like	8093131	3000116	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cep3/Upc2 domain-like	8093129	3002679	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ARM repeat-like	8093131	3000116	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Cep3/Upc2 domain-like	8093129	3002679	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	ARM repeat-like	8093131	3000116	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	ARM repeat-like	8093131	3000116	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Cep3/Upc2 domain-like	8093129	3002679	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Skp1 dimerisation domain-like	8043773	3000564	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Skp1 dimerisation domain-like	8043773	3000564	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	lambda integrase clamp domain-like	8053778	3000550	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DNA breaking-rejoining enzymes	8053766	3001127	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	DNA breaking-rejoining enzymes	8053766	3001127	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	lambda integrase clamp domain-like	8053778	3000550	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)
B	Cep3	e6gysB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Cep3	ECOD (1.6)
B	Zn_clus	e6gysB2	A: few secondary structure elements	X: Zn2/Cys6 DNA-binding domain (From Topology)	H: Zn2/Cys6 DNA-binding domain (From Topology)	T: Zn2/Cys6 DNA-binding domain	F: Zn_clus	ECOD (1.6)
C	Cep3	e6gysC1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Cep3	ECOD (1.6)
C	Zn_clus	e6gysC2	A: few secondary structure elements	X: Zn2/Cys6 DNA-binding domain (From Topology)	H: Zn2/Cys6 DNA-binding domain (From Topology)	T: Zn2/Cys6 DNA-binding domain	F: Zn_clus	ECOD (1.6)
I	Cep3	e6gysI2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Cep3	ECOD (1.6)
I	Zn_clus	e6gysI1	A: few secondary structure elements	X: Zn2/Cys6 DNA-binding domain (From Topology)	H: Zn2/Cys6 DNA-binding domain (From Topology)	T: Zn2/Cys6 DNA-binding domain	F: Zn_clus	ECOD (1.6)
J	Cep3	e6gysJ1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Cep3	ECOD (1.6)
J	Zn_clus	e6gysJ2	A: few secondary structure elements	X: Zn2/Cys6 DNA-binding domain (From Topology)	H: Zn2/Cys6 DNA-binding domain (From Topology)	T: Zn2/Cys6 DNA-binding domain	F: Zn_clus	ECOD (1.6)
D	Skp1_POZ	e6gysD1	A: a+b two layers	X: POZ domain (From Topology)	H: POZ domain (From Topology)	T: POZ domain	F: Skp1_POZ	ECOD (1.6)
K	Skp1_POZ	e6gysK1	A: a+b two layers	X: POZ domain (From Topology)	H: POZ domain (From Topology)	T: POZ domain	F: Skp1_POZ	ECOD (1.6)
E	NDC10_II_C	e6gysE1	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: NDC10_II_C	ECOD (1.6)
E	NDC10_II_N	e6gysE2	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: NDC10_II_N	ECOD (1.6)
E	Ndc10	e6gysE3	A: alpha arrays	X: lambda integrase-N-like	H: lambda integrase-N (From Topology)	T: lambda integrase-N	F: Ndc10	ECOD (1.6)
L	NDC10_II_C	e6gysL1	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: NDC10_II_C	ECOD (1.6)
L	NDC10_II_N	e6gysL3	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: NDC10_II_N	ECOD (1.6)
L	Ndc10	e6gysL2	A: alpha arrays	X: lambda integrase-N-like	H: lambda integrase-N (From Topology)	T: lambda integrase-N	F: Ndc10	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, C, I, J	PF00172	Fungal Zn(2)-Cys(6) binuclear cluster domain (Zn_clus)	Fungal Zn(2)-Cys(6) binuclear cluster domain		Domain
B, C, I, J	PF16846	Centromere DNA-binding protein complex CBF3 subunit B (Cep3)	Centromere DNA-binding protein complex CBF3 subunit B	-	Family
D, K	PF03931	Skp1 family, tetramerisation domain (Skp1_POZ)	Skp1 family, tetramerisation domain		Domain
D, K	PF01466	Skp1 family, dimerisation domain (Skp1)	Skp1 family, dimerisation domain		Domain
E, L	PF21400	Ndc10 N-terminal domain (Ndc10_N)	Ndc10 N-terminal domain	Kinetochores link centromeric DNA to spindle microtubules and ensure faithful chromosome segregation during mitosis. In point-centromere yeasts, the CBF3 complex Skp1-Ctf13-(Cep3)(2)-(Ndc10)recognizes a conserved centromeric DNA element through conta ...	Kinetochores link centromeric DNA to spindle microtubules and ensure faithful chromosome segregation during mitosis. In point-centromere yeasts, the CBF3 complex Skp1-Ctf13-(Cep3)(2)-(Ndc10)recognizes a conserved centromeric DNA element through contacts made by Cep3 and Ndc10. This entry represents the N-terminal domain of Ndc10 [1,2].	Domain
E, L	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, H	Centromere DNA-binding protein complex CBF3 subunit C	DNA binding DNA binding, bending binding nucleic acid binding	septin ring organization organelle assembly protein-containing complex organization membraneless organelle assembly septin ring assembly cellular component organization cellular component biogenesis organelle organization cellular component assembly septin cytoskeleton organization protein-containing complex assembly cellular process cellular component organization or biogenesis cytoskeleton organization septin ring organization organelle assembly protein-containing complex organization membraneless organelle assembly septin ring assembly cellular component organization cellular component biogenesis organelle organization cellular component assembly septin cytoskeleton organization protein-containing complex assembly cellular process cellular component organization or biogenesis cytoskeleton organization chromosome organization protein-DNA complex assembly protein-DNA complex organization kinetochore assembly kinetochore organization centromere complex assembly	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membraneless organelle chromosome CBF3 complex intracellular membrane-bounded organelle chromosomal region intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membraneless organelle chromosome CBF3 complex intracellular membrane-bounded organelle chromosomal region intracellular organelle cellular anatomical structure organelle membraneless organelle chromosome, centromeric region kinetochore condensed chromosome, centromeric region supramolecular complex condensed chromosome
B, C, I, J	Centromere DNA-binding protein complex CBF3 subunit B	DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding centromeric DNA binding nucleic acid binding DNA binding, bending cation binding transition metal ion binding zinc ion binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding centromeric DNA binding nucleic acid binding DNA binding, bending cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding identical protein binding protein binding	organelle assembly protein-containing complex organization chromosome organization membraneless organelle assembly protein-DNA complex assembly cellular component organization cellular component biogenesis protein-DNA complex organization organelle organization cellular component assembly kinetochore assembly protein-containing complex assembly kinetochore organization cellular process organelle assembly protein-containing complex organization chromosome organization membraneless organelle assembly protein-DNA complex assembly cellular component organization cellular component biogenesis protein-DNA complex organization organelle organization cellular component assembly kinetochore assembly protein-containing complex assembly kinetochore organization cellular process cellular component organization or biogenesis centromere complex assembly 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 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 cell cycle process mitotic nuclear division negative regulation of mitotic cell cycle phase transition organelle fission biological regulation negative regulation of cell cycle process cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling 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 metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition septin ring organization septin ring assembly septin cytoskeleton organization 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 membrane-bounded organelle 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 membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex CBF3 complex intracellular membrane-bounded organelle
D, K	Suppressor of kinetochore protein 1	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding nucleic acid binding DNA replication origin binding protein binding cullin family protein binding	regulation of biological process regulation of cellular process regulation of cellular component organization protein-containing complex organization biological regulation regulation of cellular component biogenesis cellular component biogenesis cellular component organization regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular process cellular component organization or biogenesis cell cycle regulation of biological process regulation of cellular process regulation of cellular component organization protein-containing complex organization biological regulation regulation of cellular component biogenesis cellular component biogenesis cellular component organization regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular process cellular component organization or biogenesis cell cycle mitotic cell cycle negative regulation of biological process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process translation gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of cytoplasmic translation negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process cytoplasmic translation metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of cytoplasmic translation regulation of metabolic process regulation of mitotic cell cycle regulation of cell cycle organelle fusion organelle organization mitochondrial fusion mitochondrion organization proton-transporting V-type ATPase complex assembly vacuolar proton-transporting V-type ATPase complex assembly proton-transporting two-sector ATPase complex assembly organelle assembly chromosome organization membraneless organelle assembly protein-DNA complex assembly protein-DNA complex organization kinetochore assembly kinetochore organization centromere complex assembly regulation of cell cycle phase transition cell cycle phase transition exit from mitosis cell cycle process mitotic nuclear division regulation of cell cycle process organelle fission regulation of mitotic cell cycle phase transition nuclear division mitotic cell cycle process regulation of exit from mitosis mitotic cell cycle phase transition chromatin organization chromatin remodeling heterochromatin formation epigenetic regulation of gene expression constitutive heterochromatin formation silent mating-type cassette heterochromatin formation negative regulation of gene expression, epigenetic macromolecule modification post-translational protein modification protein modification process protein neddylation protein modification by small protein conjugation protein modification by small protein conjugation or removal protein ubiquitination catabolic process proteolysis involved in protein 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 proteolysis SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process septin ring organization septin ring assembly septin cytoskeleton organization cytoskeleton organization oxoacid metabolic process sulfur amino acid metabolic process carboxylic acid metabolic process organic acid metabolic process regulation of sulfur metabolic process regulation of small molecule metabolic process sulfur compound metabolic process small molecule metabolic process regulation of sulfur amino acid metabolic process subtelomeric heterochromatin formation RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by galactose regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription G1/S transition of mitotic cell cycle cell cycle G1/S phase transition response to stimulus response to chemical cellular response to methylmercury response to methylmercury cellular response to stimulus DNA damage checkpoint signaling signaling negative regulation of cell cycle intracellular signal transduction negative regulation of mitotic cell cycle cell communication mitotic DNA integrity checkpoint signaling cellular response to stress response to stress mitotic DNA damage checkpoint signaling negative regulation of cell cycle phase transition signal transduction mitotic intra-S DNA damage checkpoint signaling DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling DNA damage response signal transduction in response to DNA damage cell cycle G2/M phase transition G2/M transition of mitotic cell cycle regulation of localization hexose transmembrane transport regulation of transport transport positive regulation of biological process carbohydrate transport establishment of localization positive regulation of D-glucose transmembrane transport transmembrane transport localization regulation of transmembrane transport positive regulation of transport D-glucose transmembrane transport positive regulation of transmembrane transport regulation of D-glucose transmembrane transport monosaccharide transmembrane transport carbohydrate transmembrane transport positive regulation of cellular process homeostatic process intracellular pH reduction regulation of intracellular pH vacuolar acidification cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis regulation of pH monoatomic ion homeostasis intracellular chemical homeostasis regulation of biological quality monoatomic cation homeostasis regulation of cellular pH intracellular monoatomic ion homeostasis	cellular anatomical structure endomembrane system protein-containing complex intracellular anatomical structure cytoplasm RAVE complex membrane-bounded organelle nucleus nuclear protein-containing complex intracellular membraneless organelle chromosome CBF3 complex intracellular membrane-bounded organelle chromosomal region cellular anatomical structure endomembrane system protein-containing complex intracellular anatomical structure cytoplasm RAVE complex membrane-bounded organelle nucleus nuclear protein-containing complex intracellular membraneless organelle chromosome CBF3 complex intracellular membrane-bounded organelle chromosomal region intracellular organelle organelle membraneless organelle chromosome, centromeric region cullin-RING ubiquitin ligase complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex kinetochore condensed chromosome, centromeric region supramolecular complex condensed chromosome chromosome, telomeric region
E, L	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 protein-DNA complex assembly cellular component organization cellular component biogenesis protein-DNA complex organization organelle organization cellular component assembly kinetochore assembly protein-containing complex assembly kinetochore organization cellular process organelle assembly protein-containing complex organization chromosome organization membraneless organelle assembly protein-DNA complex assembly cellular component organization cellular component biogenesis protein-DNA complex organization organelle organization cellular component assembly kinetochore assembly protein-containing complex assembly kinetochore organization cellular process cellular component organization or biogenesis centromere complex assembly 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 cytoplasm
F	DNA (52-MER)	-	-	-
G	DNA (52-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, H	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
B, C, I, J	IPR036864	Zn(2)-C6 fungal-type DNA-binding domain superfamily	Homologous Superfamily
B, C, I, J	IPR031760	Centromere DNA-binding protein complex CBF3 subunit B, C-terminal	Domain
B, C, I, J	IPR050613	Secondary Metabolite Biosynthesis Regulators	Family
B, C, I, J	IPR001138	Zn(2)Cys(6) fungal-type DNA-binding domain	Domain
D, K	IPR016073	SKP1 component, POZ domain	Domain
D, K	IPR001232	S-phase kinase-associated protein 1-like	Family
D, K	IPR036296	SKP1-like, dimerisation domain superfamily	Homologous Superfamily
D, K	IPR016072	SKP1 component, dimerisation	Domain
D, K	IPR011333	SKP1/BTB/POZ domain superfamily	Homologous Superfamily
D, K	IPR016897	S-phase kinase-associated protein 1	Family
E, L	IPR022210	Transcription activator GCR1-like domain	Domain
E, L	IPR049055	NDC10, N-terminal domain	Domain
E, L	IPR010998	Integrase/recombinase, N-terminal	Homologous Superfamily
E, L	IPR038279	Ndc10, domain 2 superfamily	Homologous Superfamily
E, L	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.