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- EMDB-63650: Cryo-EM structure of Arabidopsis thaliana MET1 (aa:621-1534) in c... -

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Basic information

Entry
Database: EMDB / ID: EMD-63650
TitleCryo-EM structure of Arabidopsis thaliana MET1 (aa:621-1534) in complex with hemimethylated DNA analog
Map data
Sample
  • Complex: MET1:DNA
    • 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*(A1L82)P*GP*TP*AP*AP*GP*T)-3')
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: ZINC ION
KeywordsDNA methylation / STRUCTURAL PROTEIN / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


zygote asymmetric cytokinesis in embryo sac / epigenetic programming in the endosperm / negative regulation of flower development / DNA-mediated transformation / inflorescence development / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / methyltransferase activity ...zygote asymmetric cytokinesis in embryo sac / epigenetic programming in the endosperm / negative regulation of flower development / DNA-mediated transformation / inflorescence development / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / methyltransferase activity / methylation / chromatin binding / DNA binding / nucleus
Similarity search - Function
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 ...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: 2.74 Å
AuthorsKikuchi A / Arita K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H05741, 24K01967, 24K21950 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM reveals evolutionarily conserved and distinct structural features of plant CG maintenance methyltransferase MET1.
Authors: Amika Kikuchi / Atsuya Nishiyama / Yoshie Chiba / Makoto Nakanishi / Taiko Kim To / Kyohei Arita /
Abstract: DNA methylation is essential for genomic function and transposable element silencing. In plants, DNA methylation occurs in CG, CHG, and CHH contexts (where H = A, T, or C), with the maintenance ...DNA methylation is essential for genomic function and transposable element silencing. In plants, DNA methylation occurs in CG, CHG, and CHH contexts (where H = A, T, or C), with the maintenance of CG methylation mediated by the DNA methyltransferase MET1. The molecular mechanism by which MET1 maintains CG methylation, however, remains unclear. Here, we report cryogenic electron microscopy structures of Arabidopsis thaliana MET1. We find that the methyltransferase domain of MET1 specifically methylates hemimethylated DNA in vitro. The structure of MET1 bound to hemimethylated DNA reveals the activation mechanism of MET1 resembling that of mammalian DNMT1. Curiously, the structure of apo-MET1 shows an autoinhibitory state distinct from that of DNMT1, where the RFTS2 domain and the connecting linker inhibit DNA binding. The autoinhibition of MET1 is relieved upon binding of a potential activator, ubiquitinated histone H3. Taken together, our structural analysis demonstrates both conserved and distinct molecular mechanisms regulating CG maintenance methylation in plant and animal DNA methyltransferases.
History
DepositionMar 6, 2025-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63650.png

Downloads & links

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Map

FileDownload / File: emd_63650.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 230 pix.
= 212.06 Å		0.92 Å/pix.
x 230 pix.
= 212.06 Å		0.92 Å/pix.
x 230 pix.
= 212.06 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.922 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.223
Minimum - Maximum-1.1770339 - 1.9423993
Average (Standard dev.)0.0005954027 (±0.04269438)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions230230230
Spacing230230230
CellA=B=C: 212.06 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63650_msk_1.map
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Half map: #2

Fileemd_63650_half_map_1.map
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Half map: #1

Fileemd_63650_half_map_2.map
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Sample components

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Entire : MET1:DNA

EntireName: MET1:DNA
Components
  • Complex: MET1:DNA
    • 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*(A1L82)P*GP*TP*AP*AP*GP*T)-3')
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: ZINC ION

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Supramolecule #1: MET1:DNA

SupramoleculeName: MET1:DNA / 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: 102.944789 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPLGSKRKAM QATTTRLVNR IWGEFYSNYS PEDPLQATAA ENGEDEVEEE GGNGEEEVEE EGENGLTEDT VPEPVEVQKP HTPKKIRGS SGKREIKWDG ESLGKTSAGE PLYQQALVGG EMVAVGGAVT LEVDDPDEMP AIYFVEYMFE STDHCKMLHG R FLQRGSMT ...String:
GPLGSKRKAM QATTTRLVNR IWGEFYSNYS PEDPLQATAA ENGEDEVEEE GGNGEEEVEE EGENGLTEDT VPEPVEVQKP HTPKKIRGS SGKREIKWDG ESLGKTSAGE PLYQQALVGG EMVAVGGAVT LEVDDPDEMP AIYFVEYMFE STDHCKMLHG R FLQRGSMT VLGNAANERE LFLTNECMTT QLKDIKGVAS FEIRSRPWGH QYRKKNITAD KLDWARALER KVKDLPTEYY CK SLYSPER GGFFSLPLSD IGRSSGFCTS CKIREDEEKR STIKLNVSKT GFFINGIEYS VEDFVYVNPD SIGGLKEGSK TSF KSGRNI GLRAYVVCQL LEIVPKESRK ADLGSFDVKV RRFYRPEDVS AEKAYASDIQ ELYFSQDTVV LPPGALEGKC EVRK KSDMP LSREYPISDH IFFCDLFFDT SKGSLKQLPA NMKPKFSTIK DDTLLRKKKG KGVESEIESE IVKPVEPPKE IRLAT LDIF AGCGGLSHGL KKAGVSDAKW AIEYEEPAGQ AFKQNHPEST VFVDNCNVIL RAIMEKGGDQ DDCVSTTEAN ELAAKL TEE QKSTLPLPGQ VDFINGGPPC QGFSGMNRFN QSSWSKVQCE MILAFLSFAD YFRPRYFLLE NVRTFVSFNK GQTFQLT LA SLLEMGYQVR FGILEAGAYG VSQSRKRAFI WAAAPEEVLP EWPEPMHVFG VPKLKISLSQ GLHYAAVRST ALGAPFRP I TVRDTIGDLP SVENGDSRTN KEYKEVAVSW FQKEIRGNTI ALTDHICKAM NELNLIRCKL IPTRPGADWH DLPKRKVTL SDGRVEEMIP FCLPNTAERH NGWKGLYGRL DWQGNFPTSV TDPQPMGKVG MCFHPEQHRI LTVRECARSQ GFPDSYEFAG NINHKHRQI GNAVPPPLAF ALGRKLKEAL HLKKSPQHQP

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*(A1L82)P*GP*TP*AP*AP*GP*T)-3')

MacromoleculeName: DNA (5'-D(*CP*CP*TP*TP*CP*(A1L82)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: 3.651431 KDa
SequenceString:
(DC)(DC)(DT)(DT)(DC)(A1L82)(DG)(DT)(DA)(DA) (DG)(DT)

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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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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: 60.725 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 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: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 864086
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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