6AXJ

Crystal structure of the Yaf9 YEATS domain bound to H3K27ac


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Yaf9 subunit of the NuA4 and SWR1 complexes targets histone H3K27ac through its YEATS domain.

Klein, B.J.Ahmad, S.Vann, K.R.Andrews, F.H.Mayo, Z.A.Bourriquen, G.Bridgers, J.B.Zhang, J.Strahl, B.D.Cote, J.Kutateladze, T.G.

(2018) Nucleic Acids Res 46: 421-430

  • DOI: 10.1093/nar/gkx1151
  • Primary Citation of Related Structures:  
    6AXJ

  • PubMed Abstract: 
  • Yaf9 is an integral part of the NuA4 acetyltransferase and the SWR1 chromatin remodeling complexes. Here, we show that Yaf9 associates with acetylated histone H3 with high preference for H3K27ac. The crystal structure of the Yaf9 YEATS domain bound to the H3K27ac peptide reveals that the sequence C-terminal to K27ac stabilizes the complex ...

    Yaf9 is an integral part of the NuA4 acetyltransferase and the SWR1 chromatin remodeling complexes. Here, we show that Yaf9 associates with acetylated histone H3 with high preference for H3K27ac. The crystal structure of the Yaf9 YEATS domain bound to the H3K27ac peptide reveals that the sequence C-terminal to K27ac stabilizes the complex. The side chain of K27ac inserts between two aromatic residues, mutation of which abrogates the interaction in vitro and leads in vivo to phenotypes similar to YAF9 deletion, including loss of SWR1-dependent incorporation of variant histone H2A.Z. Our findings reveal the molecular basis for the recognition of H3K27ac by a YEATS reader and underscore the importance of this interaction in mediating Yaf9 function within the NuA4 and SWR1 complexes.


    Organizational Affiliation

    Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein AF-9 homologA, C [auth B], B [auth C], D169Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YAF9YNL107WN1966
UniProt
Find proteins for P53930 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53930 
Go to UniProtKB:  P53930
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ALY-SER-ALA-PRO-ALAF [auth E], H [auth F], E [auth G], G [auth H]11Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
E [auth G], F [auth E], G [auth H], H [auth F]L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.318α = 90
b = 140.318β = 90
c = 129.054γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2017-11-29
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Database references