7XPJ

crystal structure of rice ASI1 BAH domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular basis of locus-specific H3K9 methylation catalyzed by SUVH6 in plants.

Zhang, J.Yuan, J.Lin, J.Chen, L.You, L.Y.Chen, S.Peng, L.Wang, C.H.Du, J.Duan, C.G.

(2023) Proc Natl Acad Sci U S A 120: e2208525120-e2208525120

  • DOI: https://doi.org/10.1073/pnas.2211155120
  • Primary Citation of Related Structures:  
    7XPJ, 7XPK

  • PubMed Abstract: 

    Dimethylated histone H3 Lys9 (H3K9me2) is a conserved heterochromatic mark catalyzed by SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG (SUVH) methyltransferases in plants. However, the mechanism underlying the locus specificity of SUVH enzymes has long been elusive. Here, we show that a conserved N-terminal motif is essential for SUVH6-mediated H3K9me2 deposition in planta. The SUVH6 N-terminal peptide can be recognized by the bromo-adjacent homology (BAH) domain of the RNA- and chromatin-binding protein ANTI-SILENCING 1 (ASI1), which has been shown to function in a complex to confer gene expression regulation. Structural data indicate that a classic aromatic cage of ASI1-BAH domain specifically recognizes an arginine residue of SUVH6 through extensive hydrogen bonding interactions. A classic aromatic cage of ASI1 specifically recognizes an arginine residue of SUVH6 through extensive cation-π interactions, playing a key role in recognition. The SUVH6-ASI1 module confers locus-specific H3K9me2 deposition at most SUVH6 target loci and gives rise to distinct regulation of gene expression depending on the target loci, either conferring transcriptional silencing or posttranscriptional processing of mRNA. More importantly, such mechanism is conserved in multiple plant species, indicating a coordinated evolutionary process between SUVH6 and ASI1. In summary, our findings uncover a conserved mechanism for the locus specificity of H3K9 methylation in planta. These findings provide mechanistic insights into the delicate regulation of H3K9 methylation homeostasis in plants.


  • Organizational Affiliation

    Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BAH domain-containing protein166Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: OsJ_02569
UniProt
Find proteins for B9EY07 (Oryza sativa subsp. japonica)
Explore B9EY07 
Go to UniProtKB:  B9EY07
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9EY07
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.327α = 90
b = 107.327β = 90
c = 73.362γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChinaJCYJ20200109110403829

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description