AF9 YEATS in complex with histone H3 Crotonylation at K18

Experimental Data Snapshot

  • Resolution: 2.81 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Molecular Coupling of Histone Crotonylation and Active Transcription by AF9 YEATS Domain.

Li, Y.Y.Sabari, B.R.Panchenko, T.Wen, H.Zhao, D.Guan, H.P.Wan, L.Huang, H.Tang, Z.Zhao, Y.Roeder, R.G.Shi, X.Allis, C.D.Li, H.T.

(2016) Mol Cell 62: 181-193

  • DOI: https://doi.org/10.1016/j.molcel.2016.03.028
  • Primary Citation of Related Structures:  
    5HJB, 5HJC, 5HJD

  • PubMed Abstract: 

    Recognition of histone covalent modifications by chromatin-binding protein modules ("readers") constitutes a major mechanism for epigenetic regulation, typified by bromodomains that bind acetyllysine. Non-acetyl histone lysine acylations (e.g., crotonylation, butyrylation, propionylation) have been recently identified, but readers that prefer these acylations have not been characterized. Here we report that the AF9 YEATS domain displays selectively higher binding affinity for crotonyllysine over acetyllysine. Structural studies revealed an extended aromatic sandwiching cage with crotonyl specificity arising from π-aromatic and hydrophobic interactions between crotonyl and aromatic rings. These features are conserved among the YEATS, but not the bromodomains. Using a cell-based model, we showed that AF9 co-localizes with crotonylated histone H3 and positively regulates gene expression in a YEATS domain-dependent manner. Our studies define the evolutionarily conserved YEATS domain as a family of crotonyllysine readers and specifically demonstrate that the YEATS domain of AF9 directly links histone crotonylation to active transcription.

  • Organizational Affiliation

    Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA. Electronic address: alliscd@mail.rockefeller.edu.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein AF-9140Homo sapiensMutation(s): 0 
Gene Names: MLLT3AF9YEATS3
UniProt & NIH Common Fund Data Resources
Find proteins for P42568 (Homo sapiens)
Explore P42568 
Go to UniProtKB:  P42568
GTEx:  ENSG00000171843 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42568
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
peptide of Histone H3.17Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
Entity Groups  
UniProt GroupP68431
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth G]
CA [auth K]
DA [auth N]
EA [auth N]
FA [auth Q]
AA [auth G],
CA [auth K],
DA [auth N],
EA [auth N],
FA [auth Q],
GA [auth T],
HA [auth T],
R [auth A],
U [auth C],
V [auth E],
W [auth G],
X [auth G],
Y [auth G],
Z [auth G]
O4 S
Query on CU

Download Ideal Coordinates CCD File 
BA [auth K],
Q [auth A],
S [auth C],
T [auth C]
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on KCR
I [auth L]
J [auth M]
K [auth B]
L [auth D]
M [auth F]
I [auth L],
J [auth M],
K [auth B],
L [auth D],
M [auth F],
N [auth H],
O [auth I],
P [auth J]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.81 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.264α = 90
b = 101.573β = 103.06
c = 102.076γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina91519304

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-20
    Type: Initial release
  • Version 1.1: 2016-05-04
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection