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- EMDB-64782: Cryo-EM structure of A. thaliana MET1(610-1534) bound covalently ... -

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Basic information

Entry
Database: EMDB / ID: EMD-64782
TitleCryo-EM structure of A. thaliana MET1(610-1534) bound covalently to a hemi-mCpG DNA
Map dataHalf B map of AtMET1-DNA complex with bound SAH
Sample
  • Complex: A. thaliana MET1(610-1534)-DNA complex with bound SAH
    • DNA: 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: 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')
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 1
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: ZINC ION
  • Ligand: water
KeywordsDNA methylation / MET1 / Cryo-EM structure / epigenetic regulation / GENE REGULATION/DNA / 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
DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.34 Å
AuthorsZhang Z / Li W / Liu Y / Du J
Funding support China, 1 items
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, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64782.png

Downloads & links

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Map

FileDownload / File: emd_64782.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHalf B map of AtMET1-DNA complex with bound SAH
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 273.6 Å		0.86 Å/pix.
x 320 pix.
= 273.6 Å		0.86 Å/pix.
x 320 pix.
= 273.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.009086346 - 2.0104141
Average (Standard dev.)0.0012088335 (±0.028021181)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 273.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half A map of AtMET1-DNA complex with bound SAH

Fileemd_64782_half_map_1.map
AnnotationHalf A map of AtMET1-DNA complex with bound SAH
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B map of AtMET1-DNA complex with bound SAH

Fileemd_64782_half_map_2.map
AnnotationHalf B map of AtMET1-DNA complex with bound SAH
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A. thaliana MET1(610-1534)-DNA complex with bound SAH

EntireName: A. thaliana MET1(610-1534)-DNA complex with bound SAH
Components
  • Complex: A. thaliana MET1(610-1534)-DNA complex with bound SAH
    • DNA: 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: 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')
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 1
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: A. thaliana MET1(610-1534)-DNA complex with bound SAH

SupramoleculeName: A. thaliana MET1(610-1534)-DNA complex with bound SAH / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: DNA (5'-D(*TP*AP*A*TP*GP*AP*CP*AP*TP*AP*(5CM)P*GP*AP*TP*CP*CP*AP*...

MacromoleculeName: 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')
type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.100008 KDa
SequenceString:
(DT)(DA)(DA)(DT)(DG)(DA)(DC)(DA)(DT)(DA) (5CM)(DG)(DA)(DT)(DC)(DC)(DA)(DA)(DT) (DC)

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Macromolecule #2: DNA (5'-D(*GP*AP*TP*TP*GP*GP*AP*TP*(C49)P*GP*TP*AP*TP*GP*TP*CP*AP...

MacromoleculeName: 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')
type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.243094 KDa
SequenceString:
(DG)(DA)(DT)(DT)(DG)(DG)(DA)(DT)(C49)(DG) (DT)(DA)(DT)(DG)(DT)(DC)(DA)(DT)(DT) (DA)

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Macromolecule #3: DNA (cytosine-5)-methyltransferase 1

MacromoleculeName: DNA (cytosine-5)-methyltransferase 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA (cytosine-5-)-methyltransferase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 103.673625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNPRAGMAPV ASKRKAMQAT TTRLVNRIWG EFYSNYSPED PLQATAAENG EDEVEEEGGN GEEEVEEEGE NGLTEDTVPE PVEVQKPHT PKKIRGSSGK REIKWDGESL GKTSAGEPLY QQALVGGEMV AVGGAVTLEV DDPDEMPAIY FVEYMFESTD H CKMLHGRF ...String:
SNPRAGMAPV ASKRKAMQAT TTRLVNRIWG EFYSNYSPED PLQATAAENG EDEVEEEGGN GEEEVEEEGE NGLTEDTVPE PVEVQKPHT PKKIRGSSGK REIKWDGESL GKTSAGEPLY QQALVGGEMV AVGGAVTLEV DDPDEMPAIY FVEYMFESTD H CKMLHGRF LQRGSMTVLG NAANERELFL TNECMTTQLK DIKGVASFEI RSRPWGHQYR KKNITADKLD WARALERKVK DL PTEYYCK SLYSPERGGF FSLPLSDIGR SSGFCTSCKI REDEEKRSTI KLNVSKTGFF INGIEYSVED FVYVNPDSIG GLK EGSKTS FKSGRNIGLR AYVVCQLLEI VPKESRKADL GSFDVKVRRF YRPEDVSAEK AYASDIQELY FSQDTVVLPP GALE GKCEV RKKSDMPLSR EYPISDHIFF CDLFFDTSKG SLKQLPANMK PKFSTIKDDT LLRKKKGKGV ESEIESEIVK PVEPP KEIR LATLDIFAGC GGLSHGLKKA GVSDAKWAIE YEEPAGQAFK QNHPESTVFV DNCNVILRAI MEKGGDQDDC VSTTEA NEL AAKLTEEQKS TLPLPGQVDF INGGPPCQGF SGMNRFNQSS WSKVQCEMIL AFLSFADYFR PRYFLLENVR TFVSFNK GQ TFQLTLASLL EMGYQVRFGI LEAGAYGVSQ SRKRAFIWAA APEEVLPEWP EPMHVFGVPK LKISLSQGLH YAAVRSTA L GAPFRPITVR DTIGDLPSVE NGDSRTNKEY KEVAVSWFQK EIRGNTIALT DHICKAMNEL NLIRCKLIPT RPGADWHDL PKRKVTLSDG RVEEMIPFCL PNTAERHNGW KGLYGRLDWQ GNFPTSVTDP QPMGKVGMCF HPEQHRILTV RECARSQGFP DSYEFAGNI NHKHRQIGNA VPPPLAFALG RKLKEALHLK KSPQHQP

UniProtKB: DNA (cytosine-5)-methyltransferase 1

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Macromolecule #4: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 4 / Number of copies: 1 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.34 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 861458
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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