9V4O | pdb_00009v4o

Cryo-EM structure of A. thaliana MET1 with bound SAH


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural insights into plant DNA CG methylation maintenance by MET1.

Zhang, Z.Li, W.Liu, Y.Chi, C.Nan, J.Wang, C.Zhu, Y.Zhao, J.Xue, Y.Li, Y.Wang, P.Zhai, J.Du, J.

(2025) Plant Cell 37

  • DOI: https://doi.org/10.1093/plcell/koaf244
  • Primary Citation of Related Structures:  
    9V4O, 9V4P

  • PubMed Abstract: 

    DNA methylation plays critical roles in eukaryotic gene silencing, genome defense, and the suppression of transposable elements. During DNA replication, DNA methylation is diluted and must therefore be restored through maintenance DNA methylation. In plants, in addition to symmetric CG methylation, non-CG methylation is also abundant, with the maintenance of each DNA methylation pattern employing different pathways. Here, we investigate the molecular basis of CG maintenance methylation by plant METHYLTRANSFERASE 1 (MET1), an ortholog of mammalian DNA Methyltransferase 1 (DNMT1). The cryogenic electron microscopy structure of full-length Arabidopsis (Arabidopsis thaliana) MET1 reveals a unique autoinhibitory mechanism that is distinct from that of DNMT1. The structure of the MET1 catalytic domain in complex with hemimethylated substrate DNA suggests specific recognition of hemimethylated CG DNA and reveals the catalytic mechanism. Overall, our study illuminates the molecular basis of MET1 autoinhibition and its preference for hemimethylated DNA substrates.


  • Organizational Affiliation
    • Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science and Institute for Biological Electron Microscopy, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 11,574Arabidopsis thalianaMutation(s): 0 
Gene Names: DMT1ATHIMDDM2DMT01MET1MET2At5g49160K21P3.3
EC: 2.1.1.37
UniProt
Find proteins for P34881 (Arabidopsis thaliana)
Explore P34881 
Go to UniProtKB:  P34881
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34881
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2_3874

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32325008

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release