6LSB

Crystal Structure of DPF domain of MOZ in complex with H3K14bz peptide

  • Classification: TRANSCRIPTION
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2020-01-17 Released: 2020-11-18 
  • Deposition Author(s): Li, H.T., Ren, X.L.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC), National Basic Research Program of China (973 Program)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Histone benzoylation serves as an epigenetic mark for DPF and YEATS family proteins.

Ren, X.Zhou, Y.Xue, Z.Hao, N.Li, Y.Guo, X.Wang, D.Shi, X.Li, H.

(2021) Nucleic Acids Res 49: 114-126

  • DOI: https://doi.org/10.1093/nar/gkaa1130
  • Primary Citation of Related Structures:  
    6LS6, 6LSB, 6LSD

  • PubMed Abstract: 

    Histone modifications and their functional readout serve as an important mechanism for gene regulation. Lysine benzoylation (Kbz) on histones is a recently identified acylation mark associated with active transcription. However, it remains to be explored whether putative readers exist to recognize this epigenetic mark. Here, our systematic binding studies demonstrated that the DPF and YEATS, but not the Bromodomain family members, are readers for histone Kbz. Co-crystal structural analyses revealed a 'hydrophobic encapsulation' and a 'tip-sensor' mechanism for Kbz readout by DPF and YEATS, respectively. Moreover, the DPF and YEATS family members display subtle yet unique features to create somewhat flexible engagements of different acylation marks. For instance, YEATS2 but not the other YEATS proteins exhibits best preference for Kbz than lysine acetylation and crotonylation due to its wider 'tip-sensor' pocket. The levels of histone benzoylation in cultured cells or in mice are upregulated upon sodium benzoate treatment, highlighting its dynamic regulation. In summary, our work identifies the first readers for histone Kbz and reveals the molecular basis underlying Kbz recognition, thus paving the way for further functional dissections of histone benzoylation.


  • Organizational Affiliation

    MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone acetyltransferase KAT6A131Homo sapiensMutation(s): 0 
Gene Names: MOZ
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q92794 (Homo sapiens)
Explore Q92794 
Go to UniProtKB:  Q92794
PHAROS:  Q92794
GTEx:  ENSG00000083168 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92794
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H326Homo sapiensMutation(s): 0 
UniProt
Find proteins for P22843 (Acropora formosa)
Explore P22843 
Go to UniProtKB:  P22843
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22843
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.163 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.187α = 90
b = 48.187β = 90
c = 116.848γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31725014, 31871283, 31922016
National Basic Research Program of China (973 Program)China2016YFA0500700

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references, Source and taxonomy
  • Version 1.2: 2020-12-23
    Changes: Database references
  • Version 1.3: 2021-01-27
    Changes: Database references
  • Version 1.4: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description