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- EMDB-63961: Cryo-EM structure of hemimethylated DNA-bound Tetrahymena DNA met... -

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Basic information

Entry
Database: EMDB / ID: EMD-63961
TitleCryo-EM structure of hemimethylated DNA-bound Tetrahymena DNA methyltransferase complex MTA1c
Map data
Sample
  • Complex: Tetrahymena MTA1c with hmDNA and SAM
    • Protein or peptide: mRNA m(6)A methyltransferase
    • Protein or peptide: MT-a70 family protein MTA9
    • 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 / 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 / Uncharacterized protein / mRNA m(6)A methyltransferase / Myb-like domain-containing protein
Similarity search - Component
Biological speciesTetrahymena thermophila SB210 (eukaryote) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 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 27, 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_63961.png

Downloads & links

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Map

FileDownload / File: emd_63961.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.)
0.92 Å/pix.
x 200 pix.
= 184. Å		0.92 Å/pix.
x 200 pix.
= 184. Å		0.92 Å/pix.
x 200 pix.
= 184. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.3916348 - 2.1052928
Average (Standard dev.)0.0006264964 (±0.05862056)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 184.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63961_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63961_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 with hmDNA and SAM

EntireName: Tetrahymena MTA1c with hmDNA and SAM
Components
  • Complex: Tetrahymena MTA1c with hmDNA and SAM
    • Protein or peptide: mRNA m(6)A methyltransferase
    • Protein or peptide: MT-a70 family protein MTA9
    • 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 with hmDNA and SAM

SupramoleculeName: Tetrahymena MTA1c with hmDNA 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: MT-a70 family protein MTA9

MacromoleculeName: MT-a70 family protein MTA9 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)
Molecular weightTheoretical: 55.576137 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPGRPMAPKK QEQEPIRLST RTASKKVDYL QLSNGKLEDF FDDLEEDNKP ARNRSRSKKR GRKPLKKADS RSKTPSRVSN ARGRSKSLG PRKTYPRKKN LSPDNQLSLL LKWRNDKIPL KSASETDNKC KVVNVKNIFK SDLSKYGANL QALFINALWK V KSRKEKEG ...String:
GPGRPMAPKK QEQEPIRLST RTASKKVDYL QLSNGKLEDF FDDLEEDNKP ARNRSRSKKR GRKPLKKADS RSKTPSRVSN ARGRSKSLG PRKTYPRKKN LSPDNQLSLL LKWRNDKIPL KSASETDNKC KVVNVKNIFK SDLSKYGANL QALFINALWK V KSRKEKEG LNINDLSNLK IPLSLMKNGI LFIWSEKEIL GQIVEIMEQK GFTYIENFSI MFLGLNKCLQ SINHKDEDSQ NS TASTNNT NNEAITSDLT LKDTSKFSDQ IQDNHSEDSD QARKQQTPDD ITQKKNKLLK KSSVPSIQKL FEEDPVQTPS VNK PIEKSI EQVTQEKKFV MNNLDILKST DINNLFLRNN YPYFKKTRHT LLMFRRIGDK NQKLELRHQR TSDVVFEVTD EQDP SKVDT MMKEYVYQMI ETLLPKAQFI PGVDKHLKMM ELFASTDNYR PGWISVIEKG APWSHPQFEK GGGSGGGSGG GSWSH PQFE K

UniProtKB: Uncharacterized protein

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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, 0.025% beta-OG
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400
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: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 6718 / 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: 13000
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: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 203776
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-9u9e:
Cryo-EM structure of hemimethylated DNA-bound Tetrahymena DNA methyltransferase complex MTA1c

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