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- PDB-9v4p: Cryo-EM structure of A. thaliana MET1(610-1534) bound covalently ... -

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Basic information

Entry
Database: PDB / ID: 9v4p
TitleCryo-EM structure of A. thaliana MET1(610-1534) bound covalently to a hemi-mCpG DNA
Components
  • 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')
  • 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')
  • DNA (cytosine-5)-methyltransferase 1
KeywordsGENE REGULATION/DNA / DNA methylation / MET1 / Cryo-EM structure / epigenetic regulation / GENE REGULATION-DNA complex
Function / homology
Function and homology information


zygote asymmetric cytokinesis in embryo sac / negative regulation of flower development / DNA-mediated transformation / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation / methyltransferase activity / methylation / chromatin binding / DNA binding / nucleus
Similarity search - Function
DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / : / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase ...DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / : / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.34 Å
AuthorsZhang, Z. / Li, W. / Liu, Y. / Du, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32325008 China
CitationJournal: Plant Cell / Year: 2025
Title: Structural insights into plant DNA CG methylation maintenance by MET1.
Authors: Zhihui Zhang / Wentao Li / Yue Liu / Cheng Chi / Jing Nan / Changshi Wang / Yongkun Zhu / Jun Zhao / Yan Xue / Yong Li / Peiyi Wang / Jixian Zhai / Jiamu Du /
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 ...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.
History
DepositionMay 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 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')
C: 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')
A: DNA (cytosine-5)-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4675
Polymers116,0173
Non-polymers4502
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA chain , 2 types, 2 molecules BC

#1: DNA chain 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')


Mass: 6100.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain 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')


Mass: 6243.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 1 molecules A

#3: Protein DNA (cytosine-5)-methyltransferase 1 / DNA methyltransferase 01 / DNA methyltransferase 2 / DNA methyltransferase AthI / DNA Metase AthI / ...DNA methyltransferase 01 / DNA methyltransferase 2 / DNA methyltransferase AthI / DNA Metase AthI / M.AthI / DNA methyltransferase DDM2 / Protein DECREASED DNA METHYLATION 2


Mass: 103673.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress)
Gene: DMT1, ATHIM, DDM2, DMT01, MET1, MET2, At5g49160, K21P3.3
Plasmid: pSumo / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta (DE3)
References: UniProt: P34881, DNA (cytosine-5-)-methyltransferase

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Non-polymers , 3 types, 3 molecules

#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: A. thaliana MET1(610-1534)-DNA complex with bound SAH / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Baculovirus expression vector pFastBac1-HM
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
2PHENIX1.18.2_3874model refinement
13cryoSPARC4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 861458 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0097078
ELECTRON MICROSCOPYf_angle_d0.9219713
ELECTRON MICROSCOPYf_dihedral_angle_d21.3642672
ELECTRON MICROSCOPYf_chiral_restr0.1981042
ELECTRON MICROSCOPYf_plane_restr0.0141143

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