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- EMDB-71557: Cryo-EM structure of Arabidopsis thaliana Met1 (RFTS free) -

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Basic information

Entry
Database: EMDB / ID: EMD-71557
TitleCryo-EM structure of Arabidopsis thaliana Met1 (RFTS free)
Map dataSharpened map
Sample
  • Complex: Met1
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 1
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
KeywordsDNA (cytosine-5)-methyltransferase / TRANSFERASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsLu J / Chen X / Song J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Plant Cell / Year: 2025
Title: Structure and autoinhibitory regulation of MET1 in the maintenance of plant CG methylation.
Authors: Jiuwei Lu / Xinyi Chen / Jian Fang / Daniel Li / Huy Le / Xuehua Zhong / Jikui Song /
Abstract: Plant DNA METHYLTRANSFERASE 1 (MET1) is responsible for maintaining genome-wide CG methylation. Its dysregulation has been linked to profound biological disruptions, including genomic instability and ...Plant DNA METHYLTRANSFERASE 1 (MET1) is responsible for maintaining genome-wide CG methylation. Its dysregulation has been linked to profound biological disruptions, including genomic instability and developmental defects. However, the exact mechanism by which MET1 orchestrates these vital functions and coordinates its various domains to shape the plant-specific epigenome remains unknown. Here, we report the cryo-EM structure of Arabidopsis thaliana MET1 (AtMET1), revealing an autoinhibitory mechanism that governs its DNA methylation activity. Between the two replication-foci-target sequence (RFTS) domains in AtMET1, the second RFTS domain (RFTS2) directly associates with the methyltransferase (MTase) domain, thereby inhibiting substrate-binding activity. Compared to DNMT1, AtMET1 lacks the CXXC domain and its downstream autoinhibitory linker, featuring only limited RFTS2-MTase interactions, resulting in a much-reduced autoinhibitory contact. In line with this difference, the DNA methylation activity of AtMET1 displays less temperature dependence than that of DNMT1, potentially allowing MET1 to maintain its activity across diverse temperature conditions. We further report the structure of AtMET1 bound to hemimethylated CG (hmCG) DNA, unveiling the molecular basis for substrate binding and CG recognition by AtMET1, and an activation mechanism that involves a coordinated conformational shift between two structural elements of its active site. In addition, our combined structural and biochemical analysis highlights distinct functionalities between the two RFTS domains of AtMET1, unraveling their evolutionary divergence from the DNMT1 RFTS domain. Together, this study offers a framework for understanding the structure and mechanism of AtMET1, with profound implications for the maintenance of CG methylation in plants.
History
DepositionJul 2, 2025-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71557.png

Downloads & links

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Map

FileDownload / File: emd_71557.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.96 Å/pix.
x 220 pix.
= 210.98 Å		0.96 Å/pix.
x 220 pix.
= 210.98 Å		0.96 Å/pix.
x 220 pix.
= 210.98 Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.959 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.117
Minimum - Maximum-0.584289 - 1.0578036
Average (Standard dev.)0.0001958332 (±0.023297805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 210.98 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_71557_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_71557_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_71557_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Met1

EntireName: Met1
Components
  • Complex: Met1
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 1
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE

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Supramolecule #1: Met1

SupramoleculeName: Met1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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

MacromoleculeName: DNA (cytosine-5)-methyltransferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA (cytosine-5-)-methyltransferase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 169.6695 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: STRRPRRAAA CTSFKEKSIR VCEKSATIEV KKQQIVEEEF LALRLTALET DVEDRPTRRL NDFVLFDSDG VPQPLEMLEI HDIFVSGAI LPSDVCTDKE KEKGVRCTSF GRVEHWSISG YEDGSPVIWI STELADYDCR KPAASYRKVY DYFYEKARAS V AVYKKLSK ...String:
STRRPRRAAA CTSFKEKSIR VCEKSATIEV KKQQIVEEEF LALRLTALET DVEDRPTRRL NDFVLFDSDG VPQPLEMLEI HDIFVSGAI LPSDVCTDKE KEKGVRCTSF GRVEHWSISG YEDGSPVIWI STELADYDCR KPAASYRKVY DYFYEKARAS V AVYKKLSK SSGGDPDIGL EELLAAVVRS MSSGSKYFSS GAAIIDFVIS QGDFIYNQLA GLDETAKKHE SSYVEIPVLV AL REKSSKI DKPLQRERNP SNGVRIKEVS QVAESEALTS DQLVDGTDDD RRYAILLQDE ENRKSMQQPR KNSSSGSASN MFY IKINED EIANDYPLPS YYKTSEEETD ELILYDASYE VQSEHLPHRM LHNWALYNSD LRFISLELLP MKQCDDIDVN IFGS GVVTD DNGSWISLND PDSGSQSHDP DGMCIFLSQI KEWMIEFGSD DIISISIRTD VAWYRLGKPS KLYAPWWKPV LKTAR VGIS ILTFLRVESR VARLSFADVT KRLSGLQAND KAYISSDPLA VERYLVVHGQ IILQLFAVYP DDNVKRCPFV VGLASK LED RHHTKWIIKK KKISLKELNL NPRAGMAPVA SKRKAMQATT TRLVNRIWGE FYSNYSPEDP LQATAAENGE DEVEEEG GN GEEEVEEEGE NGLTEDTVPE PVEVQKPHTP KKIRGSSGKR EIKWDGESLG KTSAGEPLYQ QALVGGEMVA VGGAVTLE V DDPDEMPAIY FVEYMFESTD HCKMLHGRFL QRGSMTVLGN AANERELFLT NECMTTQLKD IKGVASFEIR SRPWGHQYR KKNITADKLD WARALERKVK DLPTEYYCKS LYSPERGGFF SLPLSDIGRS SGFCTSCKIR EDEEKRSTIK LNVSKTGFFI NGIEYSVED FVYVNPDSIG GLKEGSKTSF KSGRNIGLRA YVVCQLLEIV PKESRKADLG SFDVKVRRFY RPEDVSAEKA Y ASDIQELY FSQDTVVLPP GALEGKCEVR KKSDMPLSRE YPISDHIFFC DLFFDTSKGS LKQLPANMKP KFSTIKDDTL LR KKKGKGV ESEIESEIVK PVEPPKEIRL ATLDIFAGCG GLSHGLKKAG VSDAKWAIEY EEPAGQAFKQ NHPESTVFVD NCN VILRAI MEKGGDQDDC VSTTEANELA AKLTEEQKST LPLPGQVDFI NGGPPCQGFS GMNRFNQSSW SKVQCEMILA FLSF ADYFR PRYFLLENVR TFVSFNKGQT FQLTLASLLE MGYQVRFGIL EAGAYGVSQS RKRAFIWAAA PEEVLPEWPE PMHVF GVPK LKISLSQGLH YAAVRSTALG APFRPITVRD TIGDLPSVEN GDSRTNKEYK EVAVSWFQKE IRGNTIALTD HICKAM NEL NLIRCKLIPT RPGADWHDLP KRKVTLSDGR VEEMIPFCLP NTAERHNGWK GLYGRLDWQG NFPTSVTDPQ PMGKVGM CF HPEQHRILTV RECARSQGFP DSYEFAGNIN HKHRQIGNAV PPPLAFALGR KLKEALHLKK SPQHQP

UniProtKB: DNA (cytosine-5)-methyltransferase 1

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 0.8 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 266522
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9pec:
Cryo-EM structure of Arabidopsis thaliana Met1 (RFTS free)

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