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- EMDB-71558: Cryo-EM structure of Arabidopsis thaliana Met1 in complex with DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-71558
TitleCryo-EM structure of Arabidopsis thaliana Met1 in complex with DNA
Map datasharpened map
Sample
  • Complex: Met1
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 1
    • DNA: DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3')
    • DNA: DNA (5'-D(*CP*CP*TP*TP*CP*(C49)P*GP*TP*AP*AP*GP*T)-3')
  • Ligand: ZINC ION
KeywordsDNA (cytosine-5)-methyltransferase / TRANSFERASE-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: 2.9 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_71558.png

Downloads & links

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Map

FileDownload / File: emd_71558.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
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 220 pix.
= 192.06 Å		0.87 Å/pix.
x 220 pix.
= 192.06 Å		0.87 Å/pix.
x 220 pix.
= 192.06 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.873 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.22
Minimum - Maximum0.0 - 21.461041999999999
Average (Standard dev.)0.21398017 (±0.7901958)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 192.06001 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_71558_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Half map: Half map A

Fileemd_71558_half_map_1.map
AnnotationHalf map A
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_71558_half_map_2.map
AnnotationHalf map B
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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
    • DNA: DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3')
    • DNA: DNA (5'-D(*CP*CP*TP*TP*CP*(C49)P*GP*TP*AP*AP*GP*T)-3')
  • Ligand: ZINC ION

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Supramolecule #1: Met1

SupramoleculeName: Met1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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: 102.334031 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SKAMQATTTR LVNRIWGEFY SNYSPEDPLQ ATAAENGEDE VEEEGGNGEE EVEEEGENGL TEDTVPEPVE VQKPHTPKKI RGSSGKREI KWDGESLGKT SAGEPLYQQA LVGGEMVAVG GAVTLEVDDP DEMPAIYFVE YMFESTDHCK MLHGRFLQRG S MTVLGNAA ...String:
SKAMQATTTR LVNRIWGEFY SNYSPEDPLQ ATAAENGEDE VEEEGGNGEE EVEEEGENGL TEDTVPEPVE VQKPHTPKKI RGSSGKREI KWDGESLGKT SAGEPLYQQA LVGGEMVAVG GAVTLEVDDP DEMPAIYFVE YMFESTDHCK MLHGRFLQRG S MTVLGNAA NERELFLTNE CMTTQLKDIK GVASFEIRSR PWGHQYRKKN ITADKLDWAR ALERKVKDLP TEYYCKSLYS PE RGGFFSL PLSDIGRSSG FCTSCKIRED EEKRSTIKLN VSKTGFFING IEYSVEDFVY VNPDSIGGLK EGSKTSFKSG RNI GLRAYV VCQLLEIVPK ESRKADLGSF DVKVRRFYRP EDVSAEKAYA SDIQELYFSQ DTVVLPPGAL EGKCEVRKKS DMPL SREYP ISDHIFFCDL FFDTSKGSLK QLPANMKPKF STIKDDTLLR KKKGKGVESE IESEIVKPVE PPKEIRLATL DIFAG CGGL SHGLKKAGVS DAKWAIEYEE PAGQAFKQNH PESTVFVDNC NVILRAIMEK GGDQDDCVST TEANELAAKL TEEQKS TLP LPGQVDFING GPPCQGFSGM NRFNQSSWSK VQCEMILAFL SFADYFRPRY FLLENVRTFV SFNKGQTFQL TLASLLE MG YQVRFGILEA GAYGVSQSRK RAFIWAAAPE EVLPEWPEPM HVFGVPKLKI SLSQGLHYAA VRSTALGAPF RPITVRDT I GDLPSVENGD SRTNKEYKEV AVSWFQKEIR GNTIALTDHI CKAMNELNLI RCKLIPTRPG ADWHDLPKRK VTLSDGRVE EMIPFCLPNT AERHNGWKGL YGRLDWQGNF PTSVTDPQPM GKVGMCFHPE QHRILTVREC ARSQGFPDSY EFAGNINHKH RQIGNAVPP PLAFALGRKL KEALHLKKSP QHQP

UniProtKB: DNA (cytosine-5)-methyltransferase 1

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Macromolecule #2: DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3')

MacromoleculeName: DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3')
type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.725469 KDa
SequenceString:
(DA)(DC)(DT)(DT)(DA)(5CM)(DG)(DG)(DA)(DA) (DG)(DG)

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Macromolecule #3: DNA (5'-D(*CP*CP*TP*TP*CP*(C49)P*GP*TP*AP*AP*GP*T)-3')

MacromoleculeName: DNA (5'-D(*CP*CP*TP*TP*CP*(C49)P*GP*TP*AP*AP*GP*T)-3')
type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.647399 KDa
SequenceString:
(DC)(DC)(DT)(DT)(DC)(A1BT7)(DG)(DT)(DA)(DA) (DG)(DT)

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 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: 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 889502
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-9ped:
Cryo-EM structure of Arabidopsis thaliana Met1 in complex with DNA

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