7EF2 | pdb_00007ef2

Crystal structure of maize SHH2 SAWADEE domain in complex with an H3K9me3 peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.245 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

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

Recognition of H3K9me1 by maize RNA-directed DNA methylation factor SHH2.

Wang, Y., Zhou, X., Luo, J., Lv, S., Liu, R., Du, X., Jia, B., Yuan, F., Zhang, H., Du, J.

(2021) J Integr Plant Biol 63: 1091-1096

  • DOI: https://doi.org/10.1111/jipb.13103
  • Primary Citation of Related Structures:  
    7EEZ, 7EF0, 7EF1, 7EF2, 7EF3

  • PubMed Abstract: 

    RNA-directed DNA methylation (RdDM) is a plant-specific de novo DNA methylation pathway, which has extensive cross-talk with histone modifications. Here, we report that the maize RdDM regulator SAWADEE HOMEODOMAIN HOMOLOG 2 (SHH2) is an H3K9me1 reader. Our structural studies reveal that H3K9me1 recognition is achieved by recognition of the methyl group via a classic aromatic cage and hydrogen-bonding and salt-bridge interactions with the free protons of the mono-methyllysine. The di- and tri-methylation states disrupt the polar interactions, decreasing the binding affinity. Our study reveals a mono-methyllysine recognition mechanism which potentially links RdDM to H3K9me1 in maize.

    • Organizational Affiliation: 
    • National Key Laboratory of Plant Molecular Genetics and Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Sciences, Shanghai, 201602, China.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HB transcription factor
A, B
158Zea maysMutation(s): 1 
Gene Names: 100279552, HB131, ZEAMMB73_Zm00001d005584
UniProt
Find proteins for B7ZYP9 (Zea mays)
Explore B7ZYP9 
Go to UniProtKB:  B7ZYP9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7ZYP9
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2C [auth P],
D [auth Q]		10Zea maysMutation(s): 0 
UniProt
Find proteins for P69246 (Zea mays)
Explore P69246 
Go to UniProtKB:  P69246
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69246
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L		C [auth P],
D [auth Q]		L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.092α = 90
b = 68.254β = 90
c = 80.811γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770782

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description