5EJO | pdb_00005ejo

Crystal structure of the winged helix domain in Chromatin assembly factor 1 subunit p90

• PDB DOI: https://doi.org/10.2210/pdb5EJO/pdb

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


• Deposited: 2015-11-02 Released: 2016-03-16 
• Deposition Author(s): Zhang, K., Gao, Y., Li, J., Burgess, R., Han, J., Liang, H., Zhang, Z., Liu, Y.
• Funding Organization(s): National Science Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.230 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

A DNA binding winged helix domain in CAF-1 functions with PCNA to stabilize CAF-1 at replication forks

Zhang, K., Gao, Y., Li, J., Burgess, R., Han, J., Liang, H., Zhang, Z., Liu, Y.

(2016) Nucleic Acids Res 44: 5083-5094

• PubMed: 26908650 
• DOI: https://doi.org/10.1093/nar/gkw106
• Primary Citation Related Structures: 
  5EJO


• PubMed Abstract: 
  

  Chromatin assembly factor 1 (CAF-1) is a histone H3-H4 chaperone that deposits newly synthesized histone (H3-H4)2 tetramers during replication-coupled nucleosome assembly. However, how CAF-1 functions in this process is not yet well understood. Here, we report the crystal structure of C terminus of Cac1 (Cac1C), a subunit of yeast CAF-1, and the function of this domain in stabilizing CAF-1 at replication forks. We show that Cac1C forms a winged helix domain (WHD) and binds DNA in a sequence-independent manner. Mutations in Cac1C that abolish DNA binding result in defects in transcriptional silencing and increased sensitivity to DNA damaging agents, and these defects are exacerbated when combined with Cac1 mutations deficient in PCNA binding. Similar phenotypes are observed for corresponding mutations in mouse CAF-1. These results reveal a mechanism conserved in eukaryotic cells whereby the ability of CAF-1 to bind DNA is important for its association with the DNA replication forks and subsequent nucleosome assembly.

---

Organizational Affiliation: 
• State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China University of the Chinese Academy of Sciences, Beijing 100049, China.
Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA.
State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China.
State Key Laboratory of Biotherapy and Cancer Center, Division of Abdominal Cancer, West China Hospital, Sichuan University, and National Collaborative innovation Center for Biotherapy, Chengdu 610041, China.
Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA [e-mail].
State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 10.55 kDa 
• Atom Count: 637 
• Modeled Residue Count: 79 
• Deposited Residue Count: 94 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin assembly factor 1 subunit p90	A	94	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: 2.75 Å
• R-Value Free:  0.230 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.655	α = 90
b = 59.655	β = 90
c = 97.408	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
SHELX	phasing
PHENIX	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-03-16 
Deposition Author(s): Zhang, K., Gao, Y., Li, J., Burgess, R., Han, J., Liang, H., Zhang, Z., Liu, Y.

---

Funding Organization	Location	Grant Number
National Science Foundation	China	30925011, 31030024 and 31021062

Revision History  

• Version 1.0: 2016-03-16
  Type: Initial release
  
• Version 1.1: 2016-07-06
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations