2VEQ | pdb_00002veq

Insights into kinetochore-DNA interactions from the structure of Cep3p

• PDB DOI: https://doi.org/10.2210/pdb2VEQ/pdb

• Classification: CELL CYCLE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-10-26 Released: 2007-12-25 
• Deposition Author(s): Purvis, A., Singleton, M.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.246 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

Insights Into Kinetochore-DNA Interactions from the Structure of Cep3Delta

Purvis, A., Singleton, M.R.

(2008) EMBO Rep 9: 56

• PubMed: 18064045 
• DOI: https://doi.org/10.1038/sj.embor.7401139
• Primary Citation Related Structures: 
  2VEQ


• PubMed Abstract: 
  

  The CBF3 complex is an essential core component of the budding yeast kinetochore and is required for the centromeric localization of all other kinetochore proteins. We determined the crystal structure of a large section of the protein Cep3 from CBF3, which is the only component with obvious DNA-binding motifs. The protein adopts a roughly bilobal shape, with an extended dimerization interface. The dimer has a large central channel that is sufficient to accommodate duplex B-form DNA. The zinc-finger domains emerge at the edges of the channel, and could bind to the DNA in a pseudo-symmetrical manner at degenerate half-sites in the centromeric sequence. We propose a mechanism for the modulation of DNA affinity by an acidic activator domain, which could be applicable to a wider family of transcription factors.

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Organizational Affiliation: 
• Macromolecular Structure and Function Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 66.59 kDa 
• Atom Count: 4,405 
• Modeled Residue Count: 520 
• Deposited Residue Count: 565 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CENTROMERE DNA-BINDING PROTEIN COMPLEX CBF3 SUBUNIT B	A	565	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40969 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40969  Go to UniProtKB:  P40969

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAC	C [auth A]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
BME	B [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.246 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.737	α = 90
b = 83.737	β = 90
c = 231.368	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-25 
Deposition Author(s): Purvis, A., Singleton, M.R.

Revision History  

• Version 1.0: 2007-12-25
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-07-12
  Changes: Refinement description
• Version 1.4: 2025-04-09
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Structure summary