8I60

Crystal structure of GAS41 YEATS domain in complex with histone H3K27cr


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.258 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Histone H3 lysine 27 crotonylation mediates gene transcriptional repression in chromatin.

Liu, N.Konuma, T.Sharma, R.Wang, D.Zhao, N.Cao, L.Ju, Y.Liu, D.Wang, S.Bosch, A.Sun, Y.Zhang, S.Ji, D.Nagatoishi, S.Suzuki, N.Kikuchi, M.Wakamori, M.Zhao, C.Ren, C.Zhou, T.J.Xu, Y.Meslamani, J.Fu, S.Umehara, T.Tsumoto, K.Akashi, S.Zeng, L.Roeder, R.G.Walsh, M.J.Zhang, Q.Zhou, M.M.

(2023) Mol Cell 83: 2206-2221.e11

  • DOI: https://doi.org/10.1016/j.molcel.2023.05.022
  • Primary Citation of Related Structures:  
    8I60

  • PubMed Abstract: 

    Histone lysine acylation, including acetylation and crotonylation, plays a pivotal role in gene transcription in health and diseases. However, our understanding of histone lysine acylation has been limited to gene transcriptional activation. Here, we report that histone H3 lysine 27 crotonylation (H3K27cr) directs gene transcriptional repression rather than activation. Specifically, H3K27cr in chromatin is selectively recognized by the YEATS domain of GAS41 in complex with SIN3A-HDAC1 co-repressors. Proto-oncogenic transcription factor MYC recruits GAS41/SIN3A-HDAC1 complex to repress genes in chromatin, including cell-cycle inhibitor p21. GAS41 knockout or H3K27cr-binding depletion results in p21 de-repression, cell-cycle arrest, and tumor growth inhibition in mice, explaining a causal relationship between GAS41 and MYC gene amplification and p21 downregulation in colorectal cancer. Our study suggests that H3K27 crotonylation signifies a previously unrecognized, distinct chromatin state for gene transcriptional repression in contrast to H3K27 trimethylation for transcriptional silencing and H3K27 acetylation for transcriptional activation.


  • Organizational Affiliation

    Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China; International Center of Future Science, Jilin University, Changchun 130012, China. Electronic address: nanliu@mail.jlu.edu.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YEATS domain-containing protein 4A [auth C],
B [auth D]
142Homo sapiensMutation(s): 0 
Gene Names: YEATS4GAS41
UniProt & NIH Common Fund Data Resources
Find proteins for O95619 (Homo sapiens)
Explore O95619 
Go to UniProtKB:  O95619
PHAROS:  O95619
GTEx:  ENSG00000127337 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95619
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-ARG-KCR-SER-ALA-PROC [auth A],
D [auth B]
13Homo 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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68431
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCR
Query on KCR
C [auth A],
D [auth B]
L-PEPTIDE LINKINGC10 H18 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.258 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.98α = 90
b = 91.98β = 90
c = 83.41γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release