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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 / 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: 2.74 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: To Be Published
Title: Cryo-EM Reveals Evolutionarily Conserved and Distinct Structural Features of Plant CG Maintenance Methyltransferase MET1
Authors: Kikuchi A / Nishiyama A / Chiba Y / Nakanishi M / To KT / Arita K
History
DepositionMar 6, 2025-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63650_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63650_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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