3FK3

Structure of the Yeats Domain, Yaf9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Asf1-like structure of the conserved Yaf9 YEATS domain and role in H2A.Z deposition and acetylation

Wang, A.Y.Schulze, J.M.Skordalakes, E.Gin, J.W.Berger, J.M.Rine, J.Kobor, M.S.

(2009) Proc Natl Acad Sci U S A 106: 21573-21578

  • DOI: https://doi.org/10.1073/pnas.0906539106
  • Primary Citation of Related Structures:  
    3FK3

  • PubMed Abstract: 

    Chromatin can be modified by posttranslational modifications of histones, ATP-dependent remodeling, and incorporation of histone variants. The Saccharomyces cerevisiae protein Yaf9 is a subunit of both the essential histone acetyltransferase complex NuA4 and the ATP-dependent chromatin remodeling complex SWR1-C, which deposits histone variant H2A.Z into euchromatin. Yaf9 contains a YEATS domain, found in proteins associated with multiple chromatin-modifying enzymes and transcription complexes across eukaryotes. Here, we established the conservation of YEATS domain function from yeast to human, and determined the structure of this region from Yaf9 by x-ray crystallography to 2.3 A resolution. The Yaf9 YEATS domain consisted of a beta-sandwich characteristic of the Ig fold and contained three distinct conserved structural features. The structure of the Yaf9 YEATS domain was highly similar to that of the histone chaperone Asf1, a similarity that extended to an ability of Yaf9 to bind histones H3 and H4 in vitro. Using structure-function analysis, we found that the YEATS domain was required for Yaf9 function, histone variant H2A.Z chromatin deposition at specific promoters, and H2A.Z acetylation.


  • Organizational Affiliation

    Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, and Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V5Z 4H4.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein AF-9 homolog
A, B, C
164Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: N1966YAF9YNL107W
UniProt
Find proteins for P53930 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53930 
Go to UniProtKB:  P53930
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53930
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.725α = 90
b = 84.725β = 90
c = 288.212γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2021-03-31
    Changes: Data collection, Database references, Derived calculations