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- EMDB-38780: Cryo-EM structure of SAH-bound Tetrahymena DNA methyltransferase ... -

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Basic information

Entry
Database: EMDB / ID: EMD-38780
TitleCryo-EM structure of SAH-bound Tetrahymena DNA methyltransferase complex MTA1c
Map data
Sample
  • Complex: Tetrahymena MTA1c with SAH
    • Protein or peptide: MT-a70 family protein
    • Protein or peptide: Methyltransferase MT, putative
    • Protein or peptide: Myb-like DNA-binding domain protein
    • Protein or peptide: Transmembrane protein, putative
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
KeywordsDNA methyltransferase / DNA N6-methyladenine modification / chromatin regulation / gene regulation / DNA BINDING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsXu Q / Shi ZB
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271264 China
CitationJournal: To Be Published
Title: Structures of Tetrahymena DNA methyltransferase MTA1c
Authors: Xu Q / Xie Y / Shi Z
History
DepositionJan 20, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38780.png

Downloads & links

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Map

FileDownload / File: emd_38780.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.)
0.92 Å/pix.
x 240 pix.
= 220.8 Å		0.92 Å/pix.
x 240 pix.
= 220.8 Å		0.92 Å/pix.
x 240 pix.
= 220.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-2.214911 - 2.8090484
Average (Standard dev.)-0.00043457083 (±0.06215413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 220.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38780_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_38780_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 : Tetrahymena MTA1c with SAH

EntireName: Tetrahymena MTA1c with SAH
Components
  • Complex: Tetrahymena MTA1c with SAH
    • Protein or peptide: MT-a70 family protein
    • Protein or peptide: Methyltransferase MT, putative
    • Protein or peptide: Myb-like DNA-binding domain protein
    • Protein or peptide: Transmembrane protein, putative
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE

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Supramolecule #1: Tetrahymena MTA1c with SAH

SupramoleculeName: Tetrahymena MTA1c with SAH / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)

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Macromolecule #1: MT-a70 family protein

MacromoleculeName: MT-a70 family protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
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: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

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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: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number real images: 3634 / Average electron dose: 48.0 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: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
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 reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 372998
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-8xyp:
Cryo-EM structure of SAH-bound Tetrahymena DNA methyltransferase complex MTA1c

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