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- PDB-10fi: apo CCAN purified from budding yeast -

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Basic information

Entry
Database: PDB / ID: 10fi
Titleapo CCAN purified from budding yeast
Components
  • (Inner kinetochore subunit ...) x 10
  • K7_Ame1p
KeywordsCELL CYCLE / Chromosome segregation / kinetochore / centromere
Function / homology
Function and homology information


negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / COMA complex / maintenance of meiotic sister chromatid cohesion / meiotic sister chromatid segregation / Mis6-Sim4 complex / establishment of meiotic sister chromatid cohesion / ascospore formation / attachment of spindle microtubules to kinetochore / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region ...negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / COMA complex / maintenance of meiotic sister chromatid cohesion / meiotic sister chromatid segregation / Mis6-Sim4 complex / establishment of meiotic sister chromatid cohesion / ascospore formation / attachment of spindle microtubules to kinetochore / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / kinetochore assembly / outer kinetochore / establishment of mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / DNA replication initiation / meiotic cell cycle / chromosome segregation / kinetochore / cell division / structural molecule activity / nucleus
Similarity search - Function
Kinetochore subunit Nkp2/Cnl2 / Cnl2/NKP2 family protein / : / CENPH protein / Centromere protein O / Cenp-O kinetochore centromere component / Centromere protein Chl4/mis15/CENP-N / Centromere protein Chl4/mis15/CENP-N
Similarity search - Domain/homology
: / Inner kinetochore subunit IML3 / Inner kinetochore subunit CHL4 / Inner kinetochore subunit MCM22 / Inner kinetochore subunit OKP1 / Inner kinetochore subunit CTF19 / Inner kinetochore subunit NKP2 / Inner kinetochore subunit MCM21 / Inner kinetochore subunit MCM16 / Inner kinetochore subunit NKP1 / Inner kinetochore subunit CTF3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMengqiu, J. / Sue, B.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Native yeast kinetochore structures identify an essential inner kinetochore interaction
Authors: Mengqiu, J. / Sue, B.
History
DepositionJan 16, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Inner kinetochore subunit MCM16
I: Inner kinetochore subunit CTF3
K: Inner kinetochore subunit MCM22
L: Inner kinetochore subunit IML3
N: Inner kinetochore subunit CHL4
O: Inner kinetochore subunit MCM21
P: Inner kinetochore subunit CTF19
Q: Inner kinetochore subunit OKP1
U: K7_Ame1p
Y: Inner kinetochore subunit NKP1
Z: Inner kinetochore subunit NKP2


Theoretical massNumber of molelcules
Total (without water)429,69511
Polymers429,69511
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Inner kinetochore subunit ... , 10 types, 10 molecules HIKLNOPQYZ

#1: Protein Inner kinetochore subunit MCM16 / CENP-H homolog / Constitutive centromere-associated network protein MCM16 / Minichromosome ...CENP-H homolog / Constitutive centromere-associated network protein MCM16 / Minichromosome maintenance protein 16


Mass: 21166.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12262
#2: Protein Inner kinetochore subunit CTF3 / CENP-I homolog / Chromosome loss protein 3 / Chromosome transmission fidelity protein 3 / ...CENP-I homolog / Chromosome loss protein 3 / Chromosome transmission fidelity protein 3 / Constitutive centromere-associated network protein CTF3


Mass: 84345.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12748
#3: Protein Inner kinetochore subunit MCM22 / CENP-K homolog / Constitutive centromere-associated network protein MCM22 / Minichromosome ...CENP-K homolog / Constitutive centromere-associated network protein MCM22 / Minichromosome maintenance protein 22


Mass: 27602.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47167
#4: Protein Inner kinetochore subunit IML3 / CENP-L homolog / Constitutive centromere-associated network protein IML3 / Increased minichromosome ...CENP-L homolog / Constitutive centromere-associated network protein IML3 / Increased minichromosome loss protein 3 / Minichromosome maintenance protein 19


Mass: 28093.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38265
#5: Protein Inner kinetochore subunit CHL4 / CENP-N homolog / Chromosome loss protein 4 / Chromosome transmission fidelity protein 17 / ...CENP-N homolog / Chromosome loss protein 4 / Chromosome transmission fidelity protein 17 / Constitutive centromere-associated network protein CHL4 / Minichromosome maintenance protein 17


Mass: 52743.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38907
#6: Protein Inner kinetochore subunit MCM21 / CENP-O homolog / Chromosome transmission fidelity protein 5 / Constitutive centromere-associated ...CENP-O homolog / Chromosome transmission fidelity protein 5 / Constitutive centromere-associated network protein MCM21 / Minichromosome maintenance protein 21


Mass: 43028.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06675
#7: Protein Inner kinetochore subunit CTF19 / CENP-P homolog / Chromosome transmission fidelity protein 19 / Constitutive centromere-associated ...CENP-P homolog / Chromosome transmission fidelity protein 19 / Constitutive centromere-associated network protein CTF19 / Minichromosome maintenance protein 18


Mass: 42841.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02732
#8: Protein Inner kinetochore subunit OKP1 / CENP-Q homolog / Constitutive centromere-associated network protein OKP1 / Outer kinetochore protein 1


Mass: 47427.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53298
#10: Protein Inner kinetochore subunit NKP1 / Constitutive centromere-associated network protein NKP1 / Non-essential kinetochore protein 1


Mass: 27006.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12493
#11: Protein Inner kinetochore subunit NKP2 / Constitutive centromere-associated network protein NKP2 / Non-essential kinetochore protein 2


Mass: 17877.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06162

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Protein , 1 types, 1 molecules U

#9: Protein K7_Ame1p


Mass: 37562.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G2W9L4

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: native purified inner kinetochore complex CCAN / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.1_5286model refinement
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48570 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00319125
ELECTRON MICROSCOPYf_angle_d0.68325878
ELECTRON MICROSCOPYf_dihedral_angle_d4.3272615
ELECTRON MICROSCOPYf_chiral_restr0.0413091
ELECTRON MICROSCOPYf_plane_restr0.0043251

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