5HJD

AF9 YEATS in complex with histone H3 Crotonylation at K18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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 1.1 of the entry. See complete history


Literature

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: 10.1016/j.molcel.2016.03.028
  • Structures With Same Primary Citation

  • 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., croto ...

    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

    MOE Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Beijing 100084, PRC; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, PRC; Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, PRC. Electronic address: lht@tsinghua.edu.cn.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein AF-9
A, C, E, G, K, N, Q, T
140Homo sapiensMutation(s): 0 
Gene Names: MLLT3AF9YEATS3
Find proteins for P42568 (Homo sapiens)
Go to UniProtKB:  P42568
NIH Common Fund Data Resources
PHAROS  P42568
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptide of Histone H3.1
B, D, F, H, I, J, L, M
7Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, C, E, G, K, N, Q, T
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CU
Query on CU

Download CCD File 
A, C, K
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCR
Query on KCR
B,D,F,H,I,J,L,ML-PEPTIDE LINKINGC10 H18 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina91519304

Revision History 

  • Version 1.0: 2016-04-20
    Type: Initial release
  • Version 1.1: 2016-05-04
    Changes: Database references