5GPL | pdb_00005gpl

Crystal structure of Ccp1

• PDB DOI: https://doi.org/10.2210/pdb5GPL/pdb

• Classification: CHAPERONE
• Organism(s): Schizosaccharomyces pombe 972h-
• Expression System: Schizosaccharomyces pombe expression vector pARG1B
• Mutation(s): No 


• Deposited: 2016-08-03 Released: 2016-11-30 
• Deposition Author(s): Yin, F., Gao, F., Chen, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.236 (Depositor) 
• R-Value Work: 
  0.193 (Depositor) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Ccp1 Homodimer Mediates Chromatin Integrity by Antagonizing CENP-A Loading

Dong, Q., Yin, F.X., Gao, F., Shen, Y., Zhang, F., Li, Y., He, H., Gonzalez, M., Yang, J., Zhang, S., Su, M., Chen, Y.H., Li, F.

(2016) Mol Cell 64: 79-91

• PubMed: 27666591 
• DOI: https://doi.org/10.1016/j.molcel.2016.08.022
• Primary Citation Related Structures: 
  5GPK, 5GPL


• PubMed Abstract: 
  

  CENP-A is a centromere-specific histone 3 variant essential for centromere specification. CENP-A partially replaces canonical histone H3 at the centromeres. How the particular CENP-A/H3 ratio at centromeres is precisely maintained is unknown. It also remains unclear how CENP-A is excluded from non-centromeric chromatin. Here, we identify Ccp1, an uncharacterized NAP family protein in fission yeast that antagonizes CENP-A loading at both centromeric and non-centromeric regions. Like the CENP-A loading factor HJURP, Ccp1 interacts with CENP-A and is recruited to centromeres at the end of mitosis in a Mis16-dependent manner. These data indicate that factors with opposing CENP-A loading activities are recruited to centromeres. Furthermore, Ccp1 also cooperates with H2A.Z to evict CENP-A assembled in euchromatin. Structural analyses indicate that Ccp1 forms a homodimer that is required for its anti-CENP-A loading activity. Our study establishes mechanisms for maintenance of CENP-A homeostasis at centromeres and the prevention of ectopic assembly of centromeres.

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Organizational Affiliation: 
• Department of Biology, New York University, New York, NY 10003, USA.
University of Chinese Academy of Sciences, Beijing 100101, China.
State Key Laboratory of Molecular Developmental Biology, CAS Center for Excellence in Biomacromolecules, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.

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 PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.71 kDa 
• Atom Count: 3,736 
• Modeled Residue Count: 412 
• Deposited Residue Count: 548 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative nucleosome assembly protein C36B7.08c	A, B	274	Schizosaccharomyces pombe 972h-	Mutation(s): 0  Gene Names: SPBC36B7.08c
UniProt
Find proteins for Q9HGN2 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q9HGN2  Go to UniProtKB:  Q9HGN2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.236 (Depositor) 
• R-Value Work:  0.193 (Depositor) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.662	α = 90
b = 86.662	β = 90
c = 158.771	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-30 
Deposition Author(s): Yin, F., Gao, F., Chen, Y.

Revision History  

• Version 1.0: 2016-11-30
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description