6LSD

Crystal Structure of YEATS domain of human YEATS2 in complex with H3K27bz 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: 2.05 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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

    Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
YEATS domain-containing protein 2A, B135Homo sapiensMutation(s): 0 
Gene Names: YEATS2KIAA1197
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULM3 (Homo sapiens)
Explore Q9ULM3 
Go to UniProtKB:  Q9ULM3
PHAROS:  Q9ULM3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ULM3
Protein Feature View
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
2C, D9Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
Entity Groups  
UniProt GroupP68431
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LBZ
Query on LBZ
C, D L-PEPTIDE LINKINGC13 H18 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.674α = 90
b = 89.674β = 90
c = 86.943γ = 90
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

  • Deposited Date: 2020-01-17 
  • Released Date: 2020-11-18 
  • Deposition Author(s): Li, H.T., Ren, X.L.

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: 2020-12-23
    Changes: Database references
  • Version 1.2: 2021-01-27
    Changes: Database references