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- PDB-6p7v: Structure of the K. lactis CBF3 core -

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Basic information

Entry
Database: PDB / ID: 6p7v
TitleStructure of the K. lactis CBF3 core
Components
  • Cep3Barrhead Airport
  • Ctf13
  • Skp1
KeywordsDNA BINDING PROTEIN / yeast centromere-binding complex
Function / homology
Function and homology information


ubiquitin-dependent protein catabolic process / DNA-binding transcription factor activity, RNA polymerase II-specific / zinc ion binding / integral component of membrane / nucleus
Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / Skp1 family, dimerisation domain / Zn(2)-C6 fungal-type DNA-binding domain profile. / Centromere DNA-binding protein complex CBF3 subunit B / Zn(2)-C6 fungal-type DNA-binding domain / S-phase kinase-associated protein 1-like / SKP1/BTB/POZ domain superfamily / SKP1 component, dimerisation / SKP1 component, POZ domain / S-phase kinase-associated protein 1 ...Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / Skp1 family, dimerisation domain / Zn(2)-C6 fungal-type DNA-binding domain profile. / Centromere DNA-binding protein complex CBF3 subunit B / Zn(2)-C6 fungal-type DNA-binding domain / S-phase kinase-associated protein 1-like / SKP1/BTB/POZ domain superfamily / SKP1 component, dimerisation / SKP1 component, POZ domain / S-phase kinase-associated protein 1 / Skp1 family, tetramerisation domain / SKP1-like, dimerisation domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Fungal Zn(2)-Cys(6) binuclear cluster domain
Centromere-associated factor / KLLA0F13816p / KLLA0D09977p
Biological speciesKluyveromyces lactis (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsLee, P.D. / Wei, H. / Tan, D. / Harrison, S.C.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute United States
National Institutes of Health/National Institute of General Medical Sciences
CitationJournal: J. Mol. Biol. / Year: 2019
Title: Structure of the Centromere Binding Factor 3 Complex from Kluyveromyces lactis.
Authors: Phong D Lee / Hui Wei / Dongyan Tan / Stephen C Harrison /
Abstract: Kinetochores are the multiprotein complexes that link chromosomal centromeres to mitotic-spindle microtubules. Budding yeast centromeres comprise three sequential "centromere-determining elements", ...Kinetochores are the multiprotein complexes that link chromosomal centromeres to mitotic-spindle microtubules. Budding yeast centromeres comprise three sequential "centromere-determining elements", CDEI, II, and III. CDEI (8 bp) and CDEIII (~25 bp) are conserved between Kluyveromyces lactis and Saccharomyces cerevisiae, but CDEII in the former is twice as long (160 bp) as CDEII in the latter (80 bp). The CBF3 complex recognizes CDEIII and is required for assembly of a centromeric nucleosome, which in turn recruits other kinetochore components. To understand differences in centromeric nucleosome assembly between K. lactis and S. cerevisiae, we determined the structure of a K. lactis CBF3 complex by electron cryomicroscopy at ~4 Å resolution and compared it with published structures of S. cerevisiae CBF3. We show differences in the pose of Ndc10 and discuss potential models of the K. lactis centromeric nucleosome that account for the extended CDEII length.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
C: Ctf13
D: Skp1
B: Cep3
A: Cep3


Theoretical massNumber of molelcules
Total (without water)215,5724
Polymers215,5724
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area7670 Å2
ΔGint-41 kcal/mol
Surface area67530 Å2

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Components

#1: Protein/peptide Ctf13 / KLLA0F13816p


Mass: 46159.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: KLLA0_F13816g / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6CK37
#2: Protein/peptide Skp1 / / Centromere-associated factor


Mass: 21081.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: SKP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O94228
#3: Protein/peptide Cep3 / Barrhead Airport / KLLA0D09977p


Mass: 74165.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: KLLA0_D09977g / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6CRD4

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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: K. lactis CBF3 core / Type: COMPLEX / Entity ID: 1,2,3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130143 / Symmetry type: POINT

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