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- EMDB-63967: Cryo-EM structure of hemi-methylated DNA-bound Tetrahymena DNA me... -

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Basic information

Entry
Database: EMDB / ID: EMD-63967
TitleCryo-EM structure of hemi-methylated DNA-bound Tetrahymena DNA methyltransferase complex MTA1c (MTA9-B)
Map data
Sample
  • Complex: Tetrahymena MTA1c (MTA9-B) with hemi-methylated DNA and SAM
    • Protein or peptide: mRNA m(6)A methyltransferase
    • Protein or peptide: Methyltransferase MT, putative
    • Protein or peptide: Myb-like DNA-binding domain protein
    • Protein or peptide: Transmembrane protein, putative
    • DNA: DNA (27-MER)
    • DNA: DNA (27-MER)
  • Ligand: S-ADENOSYLMETHIONINE
KeywordsDNA methyltransferase / DNA N6-methyladenine modification / protein-DNA complex / chromatin regulation / gene regulation / DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / methyltransferase activity / methylation / nucleus / membrane
Similarity search - Function
MT-A70-like / MT-A70 / MT-A70-like family profile. / Myb-like DNA-binding domain / SANT/Myb domain / Homeobox-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Transmembrane protein, putative / mRNA m(6)A methyltransferase / Myb-like domain-containing protein / Methyltransferase MT, putative
Similarity search - Component
Biological speciesTetrahymena thermophila SB210 (eukaryote) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsXu Q / Shi ZB
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271264 China
CitationJournal: Nat Commun / Year: 2025
Title: Mechanism for the substrate recognition by a eukaryotic DNA N-adenine methyltransferase complex.
Authors: Qi Xu / Ying Xie / Zhubing Shi /
Abstract: In eukaryotes, DNA N-methyladenine (6mA) modification plays important roles in various cellular functions, such as chromatin dynamics, gene expression regulation, and DNA damage response. It remains ...In eukaryotes, DNA N-methyladenine (6mA) modification plays important roles in various cellular functions, such as chromatin dynamics, gene expression regulation, and DNA damage response. It remains largely unknown how eukaryotic DNA 6mA methyltransferases (MTases) recognize their substrates. Here, we reported the structures of DNA-bound eukaryotic 6mA MTase complexes. The MTA1 complex (MTA1c) in ciliates is composed of MTA1, MTA9 (or MTA9-B), p1 and p2 subunits. Cryo-electron microscopy structures of MTA1c-DNA complexes reveal that DNA lies on the surface of the MTA1-MTA9/9-B dimer and is clamped by the p1 N-terminal region. The target deoxyadenosine is flipped out of the DNA duplex and approaches the catalytic center. Unmethylated and hemi-methylated DNA substrates bind MTA1c with differential conformational dynamics. Our structural and biochemical studies shed light on the activation and substrate recognition of MTA1c and provide a framework for understanding the molecular mechanism of DNA 6mA modification in eukaryotes.
History
DepositionMar 28, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63967.png

Downloads & links

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Map

FileDownload / File: emd_63967.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 240 pix.
= 258.552 Å		1.08 Å/pix.
x 240 pix.
= 258.552 Å		1.08 Å/pix.
x 240 pix.
= 258.552 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0773 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-4.951766 - 7.3872104
Average (Standard dev.)-0.0007347351 (±0.11066946)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 258.552 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63967_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63967_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Tetrahymena MTA1c (MTA9-B) with hemi-methylated DNA and SAM

EntireName: Tetrahymena MTA1c (MTA9-B) with hemi-methylated DNA and SAM
Components
  • Complex: Tetrahymena MTA1c (MTA9-B) with hemi-methylated DNA and SAM
    • Protein or peptide: mRNA m(6)A methyltransferase
    • Protein or peptide: Methyltransferase MT, putative
    • Protein or peptide: Myb-like DNA-binding domain protein
    • Protein or peptide: Transmembrane protein, putative
    • DNA: DNA (27-MER)
    • DNA: DNA (27-MER)
  • Ligand: S-ADENOSYLMETHIONINE

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Supramolecule #1: Tetrahymena MTA1c (MTA9-B) with hemi-methylated DNA and SAM

SupramoleculeName: Tetrahymena MTA1c (MTA9-B) with hemi-methylated DNA and SAM
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)

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Macromolecule #1: mRNA m(6)A methyltransferase

MacromoleculeName: mRNA m(6)A methyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: mRNA m6A methyltransferase
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)
Molecular weightTheoretical: 43.368852 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPEFKLMSKA VNKKGLRPRK SDSILDHIKN KLDQEFLEDN ENGEQSDEDY DQKSLNKAKK PYKKRQTQNG SELVISQQKT KAKASANNK KSAKNSQKLD EEEKIVEEED LSPQKNGAVS EDDQQQEAST QEDDYLDRLP KSKKGLQGLL QDIEKRILHY K QLFFKEQN ...String:
GPEFKLMSKA VNKKGLRPRK SDSILDHIKN KLDQEFLEDN ENGEQSDEDY DQKSLNKAKK PYKKRQTQNG SELVISQQKT KAKASANNK KSAKNSQKLD EEEKIVEEED LSPQKNGAVS EDDQQQEAST QEDDYLDRLP KSKKGLQGLL QDIEKRILHY K QLFFKEQN EIANGKRSMV PDNSIPICSD VTKLNFQALI DAQMRHAGKM FDVIMMDPPW QLSSSQPSRG VAIAYDSLSD EK IQNMPIQ SLQQDGFIFV WAINAKYRVT IKMIENWGYK LVDEITWVKK TVNGKIAKGH GFYLQHAKES CLIGVKGDVD NGR FKKNIA SDVIFSERRG QSQKPEEIYQ YINQLCPNGN YLEIFARRNN LHDNWVSIGN EL

UniProtKB: mRNA m(6)A methyltransferase

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Macromolecule #2: Methyltransferase MT, putative

MacromoleculeName: Methyltransferase MT, putative / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)
Molecular weightTheoretical: 41.26998 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPGRPMSQET LAACQSLDKF AHPKKVSPVQ KSQIIEEPPL QKKIKPTEPG EDQLSLLLKW RSSYIPPQKP TNEDEYKKII CKDISSEKL EQHAGDVSAL FINIKWKLSE GQSGKSIEDL KKLAISDKLI NNGIIFIWSE KEILSQIVDV LEAKGFNYIE N FMINQLSA ...String:
GPGRPMSQET LAACQSLDKF AHPKKVSPVQ KSQIIEEPPL QKKIKPTEPG EDQLSLLLKW RSSYIPPQKP TNEDEYKKII CKDISSEKL EQHAGDVSAL FINIKWKLSE GQSGKSIEDL KKLAISDKLI NNGIIFIWSE KEILSQIVDV LEAKGFNYIE N FMINQLSA DKALEMQRKN QNQQSKEKKI TDFFKRLTPQ KNIWSDITPE QCIEQEKFPP NNYVQDIFVN SEYSFFRKSK KI LLMLRKF NKDAQLELRH QRTSDIFFDI FEQNKPNDVS KKGMEFVYKM IETLLPKANY SEENKGAFKM MELYADDKSQ PRK GWISVY EQEWSHPQFE KGGGSGGGSG GGSWSHPQFE K

UniProtKB: Methyltransferase MT, putative

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Macromolecule #3: Myb-like DNA-binding domain protein

MacromoleculeName: Myb-like DNA-binding domain protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)
Molecular weightTheoretical: 41.93709 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPGRPSLKKG KFQHNQSKSL WNYTLSPGWR EEEVKILKSA LQLFGIGKWK KIMESGCLPG KSIGQIYMQT QRLLGQQSLG DFMGLQIDL EAVFNQNMKK QDVLRKNNCI INTGDNPTKE ERKRRIEQNR KIYGLSAKQI AEIKLPKVKK HAPQYMTLED I ENEKFTNL ...String:
GPGRPSLKKG KFQHNQSKSL WNYTLSPGWR EEEVKILKSA LQLFGIGKWK KIMESGCLPG KSIGQIYMQT QRLLGQQSLG DFMGLQIDL EAVFNQNMKK QDVLRKNNCI INTGDNPTKE ERKRRIEQNR KIYGLSAKQI AEIKLPKVKK HAPQYMTLED I ENEKFTNL EILTHLYNLK AEIVRRLAEQ GETIAQPSII KSLNNLNHNL EQNQNSNSST ETKVTLEQSG KKKYKVLAIE ET ELQNGPI ATNSQKKSIN GKRKNNRKIN SDSEGNEEDI SLEDIDSQES EINSEEIVED DEEDEQIEEP SKIKKRKKNP EQE SEEDDI EEDQEEDELV VNEEEIFEDD DDDEDNQDSS EDDDDDED

UniProtKB: Myb-like domain-containing protein

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Macromolecule #4: Transmembrane protein, putative

MacromoleculeName: Transmembrane protein, putative / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)
Molecular weightTheoretical: 17.04335 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPEFMKKNGK SQNQPLDFTQ YAKNMRKDLS NQDICLEDGA LNHSYFLTKK GQYWTPLNQK ALQRGIELFG VGNWKEINYD EFSGKANIV ELELRTCMIL GINDITEYYG KKISEEEQEE IKKSNIAKGK KENKLKDNIY QKLQQMQ

UniProtKB: Transmembrane protein, putative

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Macromolecule #5: DNA (27-MER)

MacromoleculeName: DNA (27-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.426495 KDa
SequenceString:
(DA)(DG)(DT)(DT)(DA)(DA)(DA)(DG)(DT)(DT) (DA)(DA)(DG)(DA)(DT)(DG)(DT)(DT)(DA)(DA) (DG)(DA)(DA)(DA)(DG)(DT)(DT)

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Macromolecule #6: DNA (27-MER)

MacromoleculeName: DNA (27-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.173334 KDa
SequenceString:
(DA)(DA)(DC)(DT)(DT)(DT)(DC)(DT)(DT)(DA) (DA)(DC)(6MA)(DT)(DC)(DT)(DT)(DA)(DA) (DC)(DT)(DT)(DT)(DA)(DA)(DC)(DT)

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Macromolecule #7: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 7 / Number of copies: 1 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE

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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

Concentration0.4 mg/mL
BufferpH: 7.5
Details: 20 mM HEPES pH 7.5, 50 mM K glutamate, 0.5 mM TCEP, 0.05% beta-OG
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 4910 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: OTHER / Details: Ab-initial model by CryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 335709
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9u9k:
Cryo-EM structure of hemi-methylated DNA-bound Tetrahymena DNA methyltransferase complex MTA1c (MTA9-B)

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