9V4P | pdb_00009v4p

Cryo-EM structure of A. thaliana MET1(610-1534) bound covalently to a hemi-mCpG DNA

• PDB DOI: https://doi.org/10.2210/pdb9V4P/pdb
• NAKB: 9V4P
• EM Map EMD-64782: EMDB EMDataResource

• Classification: GENE REGULATION/DNA
• Organism(s): synthetic construct, Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-05-24 Released: 2025-11-26 
• Deposition Author(s): Zhang, Z., Li, W., Liu, Y., Du, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.34 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 41082561 
• DOI: https://doi.org/10.1093/plcell/koaf244
• Primary Citation 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.

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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.
Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China.
State Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 116.47 kDa 
• Atom Count: 6,851 
• Modeled Residue Count: 809 
• Deposited Residue Count: 966 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5)-methyltransferase 1	C [auth A]	926	Arabidopsis thaliana	Mutation(s): 0  Gene Names: DMT1, ATHIM, DDM2, DMT01, MET1, MET2, At5g49160, K21P3.3 EC: 2.1.1.37
UniProt
Find proteins for P34881 (Arabidopsis thaliana) Explore P34881  Go to UniProtKB:  P34881

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*A*TP*GP*AP*CP*AP*TP*AP*(5CM)P*GP*AP*TP*CP*CP*AP*AP*TP*C)-3')	A [auth B]	20	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*TP*TP*GP*GP*AP*TP*(C49)P*GP*TP*AP*TP*GP*TP*CP*AP*TP*TP*A)-3')	B [auth C]	20	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	D [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.34 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.18.2_3874
RECONSTRUCTION	cryoSPARC	4.5.3

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Zhang, Z., Li, W., Liu, Y., Du, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32325008

Revision History  

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