5HJC

BRD3 second bromodomain in complex with histone H3 acetylation at K18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: 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

    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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 3110Homo sapiensMutation(s): 0 
Gene Names: BRD3KIAA0043RING3L
UniProt & NIH Common Fund Data Resources
Find proteins for Q15059 (Homo sapiens)
Explore Q15059 
Go to UniProtKB:  Q15059
PHAROS:  Q15059
GTEx:  ENSG00000169925 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15059
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
peptide of Histone H3.19Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
Entity Groups  
UniProt GroupP68431
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ALY
Query on ALY
B
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.768α = 90
b = 79.768β = 90
c = 95.262γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
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  (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