6F07 | pdb_00006f07

CBF3 Core Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Structural basis for assembly of the CBF3 kinetochore complex.

Leber, V.Nans, A.Singleton, M.R.

(2018) EMBO J 37: 269-281

  • DOI: https://doi.org/10.15252/embj.201798134
  • Primary Citation Related Structures: 
    6F07

  • PubMed Abstract: 

    Eukaryotic chromosomes contain a specialised region known as the centromere, which forms the platform for kinetochore assembly and microtubule attachment. The centromere is distinguished by the presence of nucleosomes containing the histone H3 variant, CENP-A. In budding yeast, centromere establishment begins with the recognition of a specific DNA sequence by the CBF3 complex. This in turn facilitates CENP-A Cse4 nucleosome deposition and kinetochore assembly. Here, we describe a 3.6 Å single-particle cryo-EM reconstruction of the core CBF3 complex, incorporating the sequence-specific DNA-binding protein Cep3 together with regulatory subunits Ctf13 and Skp1. This provides the first structural data on Ctf13, defining it as an F-box protein of the leucine-rich-repeat family, and demonstrates how a novel F-box-mediated interaction between Ctf13 and Skp1 is responsible for initial assembly of the CBF3 complex.


  • Organizational Affiliation
    • Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK.

Macromolecule Content 

  • Total Structure Weight: 167.76 kDa 
  • Atom Count: 10,149 
  • Modeled Residue Count: 1,227 
  • Deposited Residue Count: 1,434 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere DNA-binding protein complex CBF3 subunit B
A, B
620Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CEP3CBF3CBF3BCSL1YMR168CYM8520.17C
UniProt
Find proteins for P40969 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40969 
Go to UniProtKB:  P40969
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40969
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Suppressor of kinetochore protein 1C [auth D]194Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SKP1CBF3DYDR328CD9798.14
UniProt
Find proteins for P52286 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P52286 
Go to UniProtKB:  P52286
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52286
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.12
RECONSTRUCTIONRELION2.1.1

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomFC001155
Medical Research Council (United Kingdom)United KingdomFC001155
Wellcome TrustUnited KingdomFC001155

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2017-12-20
    Changes: Database references
  • Version 1.2: 2018-01-31
    Changes: Database references
  • Version 1.3: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2019-12-11
    Changes: Other
  • Version 1.5: 2024-10-09
    Changes: Data collection, Database references, Structure summary