4EO5

Yeast Asf1 bound to H3/H4G94P mutant

• PDB DOI: https://doi.org/10.2210/pdb4EO5/pdb

• Classification: STRUCTURAL PROTEIN/CHAPERONE
• Organism(s): Saccharomyces cerevisiae, Xenopus laevis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-04-13 Released: 2012-06-13 
• Deposition Author(s): Scorgie, J.K., Churchill, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.240 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

The conformational flexibility of the C-terminus of histone H4 promotes histone octamer and nucleosome stability and yeast viability.

Chavez, M.S., Scorgie, J.K., Dennehey, B.K., Noone, S.M., Tyler, J.K., Churchill, M.E.

(2012) Epigenetics Chromatin 5: 5-5

• PubMed: 22541333 
• DOI: https://doi.org/10.1186/1756-8935-5-5
• Primary Citation of Related Structures:  
  4EO5


• PubMed Abstract: 
  

  The protein anti-silencing function 1 (Asf1) chaperones histones H3/H4 for assembly into nucleosomes every cell cycle as well as during DNA transcription and repair. Asf1 interacts directly with H4 through the C-terminal tail of H4, which itself interacts with the docking domain of H2A in the nucleosome. The structure of this region of the H4 C-terminus differs greatly in these two contexts.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 37.51 kDa 
• Atom Count: 2,844 
• Modelled Residue Count: 320 
• Deposited Residue Count: 328 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone chaperone ASF1	A	169	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: ASF1, CIA1, YJL115W, J0755
UniProt
Find proteins for P32447 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32447  Go to UniProtKB:  P32447

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	B	76	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233  Go to UniProtKB:  P84233

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	C	83	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799  Go to UniProtKB:  P62799

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	D [auth A], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.240 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.691	α = 90
b = 97.691	β = 90
c = 115.072	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-13 
Deposition Author(s): Scorgie, J.K., Churchill, M.E.

Revision History  

• Version 1.0: 2012-06-13
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description