4TMP

Crystal structure of AF9 YEATS bound to H3K9ac peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

AF9 YEATS Domain Links Histone Acetylation to DOT1L-Mediated H3K79 Methylation.

Li, Y.Wen, H.Xi, Y.Tanaka, K.Wang, H.Peng, D.Ren, Y.Jin, Q.Dent, S.Y.Li, W.Li, H.Shi, X.

(2014) Cell 159: 558-571

  • DOI: 10.1016/j.cell.2014.09.049
  • Primary Citation of Related Structures:  
    4TMP

  • PubMed Abstract: 
  • The recognition of modified histones by "reader" proteins constitutes a key mechanism regulating gene expression in the chromatin context. Compared with the great variety of readers for histone methylation, few protein modules that recognize histone acetylation are known ...

    The recognition of modified histones by "reader" proteins constitutes a key mechanism regulating gene expression in the chromatin context. Compared with the great variety of readers for histone methylation, few protein modules that recognize histone acetylation are known. Here, we show that the AF9 YEATS domain binds strongly to histone H3K9 acetylation and, to a lesser extent, H3K27 and H3K18 acetylation. Crystal structural studies revealed that AF9 YEATS adopts an eight-stranded immunoglobin fold and utilizes a serine-lined aromatic "sandwiching" cage for acetyllysine readout, representing a novel recognition mechanism that is distinct from that of known acetyllysine readers. ChIP-seq experiments revealed a strong colocalization of AF9 and H3K9 acetylation genome-wide, which is important for the chromatin recruitment of the H3K79 methyltransferase DOT1L. Together, our studies identified the evolutionarily conserved YEATS domain as a novel acetyllysine-binding module and established a direct link between histone acetylation and DOT1L-mediated H3K79 methylation in transcription control.


    Organizational Affiliation

    Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA; Genes and Development and Molecular Carcinogenesis Graduate Programs, The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA. Electronic address: xbshi@mdanderson.org.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein AF-9A, C141Homo sapiensMutation(s): 0 
Gene Names: MLLT3AF9YEATS3
UniProt & NIH Common Fund Data Resources
Find proteins for P42568 (Homo sapiens)
Explore P42568 
Go to UniProtKB:  P42568
PHAROS:  P42568
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ALA-ARG-THR-LYS-GLN-THR-ALA-ARG-ALY-SER-THRB, D11Homo sapiensMutation(s): 0 
Gene Names: H3-3AH3.3AH3F3H3F3APP781H3-3BH3.3BH3F3B
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens)
Explore P84243 
Go to UniProtKB:  P84243
PHAROS:  P84243
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A], F [auth C], G [auth C], H [auth C]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
B, DL-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.166 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.537α = 90
b = 195.704β = 90
c = 106.675γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2011CB965300

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2014-12-31
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2020-01-08
    Changes: Author supporting evidence