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- EMDB-63652: Cryo-EM structure of Arabidopsis thaliana MET1 -

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Basic information

Entry
Database: EMDB / ID: EMD-63652
TitleCryo-EM structure of Arabidopsis thaliana MET1
Map data
Sample
  • Complex: MET1
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 1
  • Ligand: ZINC ION
KeywordsDNA methylation / STRUCTURAL PROTEIN
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: 3.21 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_63652.png

Downloads & links

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Map

FileDownload / File: emd_63652.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 200 pix.
= 212.096 Å		1.06 Å/pix.
x 200 pix.
= 212.096 Å		1.06 Å/pix.
x 200 pix.
= 212.096 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.133
Minimum - Maximum-0.751879 - 1.19927
Average (Standard dev.)0.0008989124 (±0.029697908)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 212.096 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63652_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63652_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_63652_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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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

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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: 173.114438 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPPTTMVENG AKAAKRKKRP LPEIQEVEDV PRTRRPRRAA ACTSFKEKSI RVCEKSATIE VKKQQIVEEE FLALRLTALE TDVEDRPTR RLNDFVLFDS DGVPQPLEML EIHDIFVSGA ILPSDVCTDK EKEKGVRCTS FGRVEHWSIS GYEDGSPVIW I STELADYD ...String:
GPPTTMVENG AKAAKRKKRP LPEIQEVEDV PRTRRPRRAA ACTSFKEKSI RVCEKSATIE VKKQQIVEEE FLALRLTALE TDVEDRPTR RLNDFVLFDS DGVPQPLEML EIHDIFVSGA ILPSDVCTDK EKEKGVRCTS FGRVEHWSIS GYEDGSPVIW I STELADYD CRKPAASYRK VYDYFYEKAR ASVAVYKKLS KSSGGDPDIG LEELLAAVVR SMSSGSKYFS SGAAIIDFVI SQ GDFIYNQ LAGLDETAKK HESSYVEIPV LVALREKSSK IDKPLQRERN PSNGVRIKEV SQVAESEALT SDQLVDGTDD DRR YAILLQ DEENRKSMQQ PRKNSSSGSA SNMFYIKINE DEIANDYPLP SYYKTSEEET DELILYDASY EVQSEHLPHR MLHN WALYN SDLRFISLEL LPMKQCDDID VNIFGSGVVT DDNGSWISLN DPDSGSQSHD PDGMCIFLSQ IKEWMIEFGS DDIIS ISIR TDVAWYRLGK PSKLYAPWWK PVLKTARVGI SILTFLRVES RVARLSFADV TKRLSGLQAN DKAYISSDPL AVERYL VVH GQIILQLFAV YPDDNVKRCP FVVGLASKLE DRHHTKWIIK KKKISLKELN LNPRAGMAPV ASKRKAMQAT TTRLVNR IW GEFYSNYSPE DPLQATAAEN GEDEVEEEGG NGEEEVEEEG ENGLTEDTVP EPVEVQKPHT PKKIRGSSGK REIKWDGE S LGKTSAGEPL YQQALVGGEM VAVGGAVTLE VDDPDEMPAI YFVEYMFEST DHCKMLHGRF LQRGSMTVLG NAANERELF LTNECMTTQL KDIKGVASFE IRSRPWGHQY RKKNITADKL DWARALERKV KDLPTEYYCK SLYSPERGGF FSLPLSDIGR SSGFCTSCK IREDEEKRST IKLNVSKTGF FINGIEYSVE DFVYVNPDSI GGLKEGSKTS FKSGRNIGLR AYVVCQLLEI V PKESRKAD LGSFDVKVRR FYRPEDVSAE KAYASDIQEL YFSQDTVVLP PGALEGKCEV RKKSDMPLSR EYPISDHIFF CD LFFDTSK GSLKQLPANM KPKFSTIKDD TLLRKKKGKG VESEIESEIV KPVEPPKEIR LATLDIFAGC GGLSHGLKKA GVS DAKWAI EYEEPAGQAF KQNHPESTVF VDNCNVILRA IMEKGGDQDD CVSTTEANEL AAKLTEEQKS TLPLPGQVDF INGG PPCQG FSGMNRFNQS SWSKVQCEMI LAFLSFADYF RPRYFLLENV RTFVSFNKGQ TFQLTLASLL EMGYQVRFGI LEAGA YGVS QSRKRAFIWA AAPEEVLPEW PEPMHVFGVP KLKISLSQGL HYAAVRSTAL GAPFRPITVR DTIGDLPSVE NGDSRT NKE YKEVAVSWFQ KEIRGNTIAL TDHICKAMNE LNLIRCKLIP TRPGADWHDL PKRKVTLSDG RVEEMIPFCL PNTAERH NG WKGLYGRLDW QGNFPTSVTD PQPMGKVGMC FHPEQHRILT VRECARSQGF PDSYEFAGNI NHKHRQIGNA VPPPLAFA L GRKLKEALHL KKSPQHQP

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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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: 54.1 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: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 307752
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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