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- EMDB-64781: Cryo-EM structure of A. thaliana MET1 with bound SAH -

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Basic information

Entry
Database: EMDB / ID: EMD-64781
TitleCryo-EM structure of A. thaliana MET1 with bound SAH
Map datamap of AtMET1 with bound SAH
Sample
  • Complex: DNA (cytosine-5)-methyltransferase 1
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 1
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: ZINC ION
KeywordsDNA methylation / covalent AtMET1-DNA complex / Cryo-EM structure / epigenetic regulation / GENE REGULATION
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: 2.92 Å
AuthorsZhang Z / Liu Y / Li W / 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_64781.png

Downloads & links

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Map

FileDownload / File: emd_64781.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of AtMET1 with bound SAH
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.1
Minimum - Maximum-0.18259723 - 19.216439999999999
Average (Standard dev.)-0.051940806 (±0.4590429)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half B map of AtMET1 with bound SAH

Fileemd_64781_half_map_1.map
AnnotationHalf B map of AtMET1 with bound SAH
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half A map of AtMET1 with bound SAH

Fileemd_64781_half_map_2.map
AnnotationHalf A map of AtMET1 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 : DNA (cytosine-5)-methyltransferase 1

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

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

SupramoleculeName: DNA (cytosine-5)-methyltransferase 1 / 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
Details: tag(1-40)+DNA (cytosine-5)-methyltransferase 1(41-1574)
Number of copies: 1 / Enantiomer: LEVO / EC number: DNA (cytosine-5-)-methyltransferase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 177.588062 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MSYYHHHHHH HHHHDYDIDY KDDDDKPTTE NLYFQGAMGS MVENGAKAAK RKKRPLPEIQ EVEDVPRTRR PRRAAACTSF KEKSIRVCE KSATIEVKKQ QIVEEEFLAL RLTALETDVE DRPTRRLNDF VLFDSDGVPQ PLEMLEIHDI FVSGAILPSD V CTDKEKEK ...String:
MSYYHHHHHH HHHHDYDIDY KDDDDKPTTE NLYFQGAMGS MVENGAKAAK RKKRPLPEIQ EVEDVPRTRR PRRAAACTSF KEKSIRVCE KSATIEVKKQ QIVEEEFLAL RLTALETDVE DRPTRRLNDF VLFDSDGVPQ PLEMLEIHDI FVSGAILPSD V CTDKEKEK GVRCTSFGRV EHWSISGYED GSPVIWISTE LADYDCRKPA ASYRKVYDYF YEKARASVAV YKKLSKSSGG DP DIGLEEL LAAVVRSMSS GSKYFSSGAA IIDFVISQGD FIYNQLAGLD ETAKKHESSY VEIPVLVALR EKSSKIDKPL QRE RNPSNG VRIKEVSQVA ESEALTSDQL VDGTDDDRRY AILLQDEENR KSMQQPRKNS SSGSASNMFY IKINEDEIAN DYPL PSYYK TSEEETDELI LYDASYEVQS EHLPHRMLHN WALYNSDLRF ISLELLPMKQ CDDIDVNIFG SGVVTDDNGS WISLN DPDS GSQSHDPDGM CIFLSQIKEW MIEFGSDDII SISIRTDVAW YRLGKPSKLY APWWKPVLKT ARVGISILTF LRVESR VAR LSFADVTKRL SGLQANDKAY ISSDPLAVER YLVVHGQIIL QLFAVYPDDN VKRCPFVVGL ASKLEDRHHT KWIIKKK KI SLKELNLNPR AGMAPVASKR KAMQATTTRL VNRIWGEFYS NYSPEDPLQA TAAENGEDEV EEEGGNGEEE VEEEGENG L TEDTVPEPVE VQKPHTPKKI RGSSGKREIK WDGESLGKTS AGEPLYQQAL VGGEMVAVGG AVTLEVDDPD EMPAIYFVE YMFESTDHCK MLHGRFLQRG SMTVLGNAAN ERELFLTNEC MTTQLKDIKG VASFEIRSRP WGHQYRKKNI TADKLDWARA LERKVKDLP TEYYCKSLYS PERGGFFSLP LSDIGRSSGF CTSCKIREDE EKRSTIKLNV SKTGFFINGI EYSVEDFVYV N PDSIGGLK EGSKTSFKSG RNIGLRAYVV CQLLEIVPKE SRKADLGSFD VKVRRFYRPE DVSAEKAYAS DIQELYFSQD TV VLPPGAL EGKCEVRKKS DMPLSREYPI SDHIFFCDLF FDTSKGSLKQ LPANMKPKFS TIKDDTLLRK KKGKGVESEI ESE IVKPVE PPKEIRLATL DIFAGCGGLS HGLKKAGVSD AKWAIEYEEP AGQAFKQNHP ESTVFVDNCN VILRAIMEKG GDQD DCVST TEANELAAKL TEEQKSTLPL PGQVDFINGG PPCQGFSGMN RFNQSSWSKV QCEMILAFLS FADYFRPRYF LLENV RTFV SFNKGQTFQL TLASLLEMGY QVRFGILEAG AYGVSQSRKR AFIWAAAPEE VLPEWPEPMH VFGVPKLKIS LSQGLH YAA VRSTALGAPF RPITVRDTIG DLPSVENGDS RTNKEYKEVA VSWFQKEIRG NTIALTDHIC KAMNELNLIR CKLIPTR PG ADWHDLPKRK VTLSDGRVEE MIPFCLPNTA ERHNGWKGLY GRLDWQGNFP TSVTDPQPMG KVGMCFHPEQ HRILTVRE C ARSQGFPDSY EFAGNINHKH RQIGNAVPPP LAFALGRKLK EALHLKKSPQ HQP

UniProtKB: DNA (cytosine-5)-methyltransferase 1

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Macromolecule #2: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 2 / 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 #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / 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 BIOQUANTUM (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: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 629218
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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