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
View more details

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
Find similar proteins by: 
(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
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

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
Expand
  • 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

View Full Validation Report



View more in-depth experimental data
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