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- PDB-10eh: De novo assembled CBF3-CEN complex -

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Basic information

Entry
Database: PDB / ID: 10eh
TitleDe novo assembled CBF3-CEN complex
Components
  • (Centromere DNA-binding protein complex CBF3 subunit ...) x 3
  • (DNA (44-MER)) x 2
  • Suppressor of kinetochore protein 1
KeywordsCELL CYCLE/DNA / chromosome segregation / kinetochore / centromere / CELL CYCLE / CELL CYCLE-DNA complex
Function / homology
Function and homology information


RAVE complex / Iron uptake and transport / : / CBF3 complex / regulation of transcription by galactose / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / septin ring assembly / mitotic spindle elongation / centromeric DNA binding ...RAVE complex / Iron uptake and transport / : / CBF3 complex / regulation of transcription by galactose / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / septin ring assembly / mitotic spindle elongation / centromeric DNA binding / regulation of exit from mitosis / kinetochore assembly / condensed chromosome, centromeric region / spindle pole body / positive regulation of D-glucose transmembrane transport / vacuolar acidification / exit from mitosis / protein neddylation / mitochondrial fusion / mitotic intra-S DNA damage checkpoint signaling / silent mating-type cassette heterochromatin formation / DNA binding, bending / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / SCF ubiquitin ligase complex / mitotic spindle assembly checkpoint signaling / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Orc1 removal from chromatin / spindle midzone / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / DNA replication origin binding / regulation of protein-containing complex assembly / cullin family protein binding / subtelomeric heterochromatin formation / negative regulation of cytoplasmic translation / endomembrane system / regulation of mitotic cell cycle / chromosome segregation / G1/S transition of mitotic cell cycle / kinetochore / G2/M transition of mitotic cell cycle / spindle / mitotic cell cycle / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / DNA-binding transcription factor activity, RNA polymerase II-specific / chromosome, telomeric region / protein ubiquitination / DNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / Ndc10 N-terminal domain / Transcription activator GCR1-like domain / Ndc10, domain 2 / Ndc10, domain 2 superfamily / Transcriptional activator of glycolytic enzymes / Centromere DNA-binding protein complex CBF3 subunit, domain 2 / : / Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / Centromere DNA-binding protein complex CBF3 subunit B ...: / Ndc10 N-terminal domain / Transcription activator GCR1-like domain / Ndc10, domain 2 / Ndc10, domain 2 superfamily / Transcriptional activator of glycolytic enzymes / Centromere DNA-binding protein complex CBF3 subunit, domain 2 / : / Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / Centromere DNA-binding protein complex CBF3 subunit B / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / Integrase/recombinase, N-terminal / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Centromere DNA-binding protein complex CBF3 subunit A / Centromere DNA-binding protein complex CBF3 subunit C / Centromere DNA-binding protein complex CBF3 subunit B / Suppressor of kinetochore protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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 15, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 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

Downloads & links

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Assembly

Deposited unit
A: Centromere DNA-binding protein complex CBF3 subunit A
B: Centromere DNA-binding protein complex CBF3 subunit B
C: Centromere DNA-binding protein complex CBF3 subunit B
D: Centromere DNA-binding protein complex CBF3 subunit C
E: Suppressor of kinetochore protein 1
F: DNA (44-MER)
G: DNA (44-MER)
H: Centromere DNA-binding protein complex CBF3 subunit A
I: Centromere DNA-binding protein complex CBF3 subunit A
J: Centromere DNA-binding protein complex CBF3 subunit A
a: Centromere DNA-binding protein complex CBF3 subunit A
b: Centromere DNA-binding protein complex CBF3 subunit B
c: Centromere DNA-binding protein complex CBF3 subunit B
d: Centromere DNA-binding protein complex CBF3 subunit C
e: Suppressor of kinetochore protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,317,40616
Polymers1,317,34015
Non-polymers651
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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Centromere DNA-binding protein complex CBF3 subunit ... , 3 types, 11 molecules AHIJaBCbcDd

#1: Protein
Centromere DNA-binding protein complex CBF3 subunit A / Centromere-binding factor 2 / Chromosome transmission fidelity protein 14 / Kinetochore protein CTF14


Mass: 112066.031 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32504
#2: Protein
Centromere DNA-binding protein complex CBF3 subunit B / Centromere protein 3


Mass: 71439.891 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40969
#3: Protein Centromere DNA-binding protein complex CBF3 subunit C / Chromosome transmission fidelity protein 13 / Kinetochore protein CTF13


Mass: 56416.863 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35203

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DNA chain , 2 types, 2 molecules FG

#5: DNA chain DNA (44-MER)


Mass: 157288.578 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (44-MER)


Mass: 156413.875 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / Non-polymers , 2 types, 3 molecules Ee

#4: Protein Suppressor of kinetochore protein 1 / Centromere DNA-binding protein complex CBF3 subunit D / E3 ubiquitin ligase complex SCF subunit SKP1


Mass: 22357.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P52286
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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: CBF3-CEN complex / Type: COMPLEX / Entity ID: #1-#6 / Source: MULTIPLE SOURCES
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
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64688 / Symmetry type: POINT
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00441311
ELECTRON MICROSCOPYf_angle_d0.5756266
ELECTRON MICROSCOPYf_dihedral_angle_d15.526240
ELECTRON MICROSCOPYf_chiral_restr0.0396191
ELECTRON MICROSCOPYf_plane_restr0.0046818

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