5JBM | pdb_00005jbm

Crystal structgure of Cac1 C-terminus

• PDB DOI: https://doi.org/10.2210/pdb5JBM/pdb

• Classification: CHAPERONE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-04-13 Released: 2016-10-26 
• Deposition Author(s): Churchill, M.E.A., Liu, W., Zhou, Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.275 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

The Cac1 subunit of histone chaperone CAF-1 organizes CAF-1-H3/H4 architecture and tetramerizes histones.

Liu, W.H., Roemer, S.C., Zhou, Y., Shen, Z.J., Dennehey, B.K., Balsbaugh, J.L., Liddle, J.C., Nemkov, T., Ahn, N.G., Hansen, K.C., Tyler, J.K., Churchill, M.E.

(2016) Elife 5

• PubMed: 27690308 
• DOI: https://doi.org/10.7554/eLife.18023
• Primary Citation Related Structures: 
  5JBM


• PubMed Abstract: 
  

  The histone chaperone Chromatin Assembly Factor 1 (CAF-1) deposits tetrameric (H3/H4) ₂ histones onto newly-synthesized DNA during DNA replication. To understand the mechanism of the tri-subunit CAF-1 complex in this process, we investigated the protein-protein interactions within the CAF-1-H3/H4 architecture using biophysical and biochemical approaches. Hydrogen/deuterium exchange and chemical cross-linking coupled to mass spectrometry reveal interactions that are essential for CAF-1 function in budding yeast, and importantly indicate that the Cac1 subunit functions as a scaffold within the CAF-1-H3/H4 complex. Cac1 alone not only binds H3/H4 with high affinity, but also promotes histone tetramerization independent of the other subunits. Moreover, we identify a minimal region in the C-terminus of Cac1, including the structured winged helix domain and glutamate/aspartate-rich domain, which is sufficient to induce (H3/H4) ₂ tetramerization. These findings reveal a key role of Cac1 in histone tetramerization, providing a new model for CAF-1-H3/H4 architecture and function during eukaryotic replication.

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Organizational Affiliation: 
• Department of Pharmacology, University of Colorado School of Medicine, Aurora, United States.
Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, United States.
Department of Epigenetics and Molecular Carcinogenesis, MD Anderson Cancer Center, Houston, United States.
Department of Chemistry and Biochemistry, University of Colorado, Boulder, Boulder, United States.
BioFrontiers Institute, University of Colorado, Boulder, Boulder, United States.
Program in Structural Biology and Biochemistry, University of Colorado School of Medicine, Aurora, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.96 kDa 
• Atom Count: 654 
• Modeled Residue Count: 81 
• Deposited Residue Count: 150 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin assembly factor 1 subunit p90	A	150	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RLF2, CAC1, YPR018W, YP9531.12
UniProt
Find proteins for Q12495 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12495  Go to UniProtKB:  Q12495

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.275 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.85	α = 90
b = 58.85	β = 90
c = 97.929	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-10-26 
Deposition Author(s): Churchill, M.E.A., Liu, W., Zhou, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM111902-02

Revision History  

• Version 1.0: 2016-10-26
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description