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- PDB-9u9e: Cryo-EM structure of hemimethylated DNA-bound Tetrahymena DNA met... -

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Basic information

Entry
Database: PDB / ID: 9u9e
TitleCryo-EM structure of hemimethylated DNA-bound Tetrahymena DNA methyltransferase complex MTA1c
Components
  • (DNA (27-MER)) x 2
  • MT-a70 family protein MTA9
  • Myb-like DNA-binding domain protein
  • Transmembrane protein, putative
  • mRNA m(6)A methyltransferase
KeywordsDNA BINDING PROTEIN/DNA / DNA methyltransferase / DNA N6-methyladenine modification / protein-DNA complex / chromatin regulation / gene regulation / 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
S-ADENOSYLMETHIONINE / DNA / DNA (> 10) / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsXu, Q. / Shi, Z.B.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mRNA m(6)A methyltransferase
B: MT-a70 family protein MTA9
C: Myb-like DNA-binding domain protein
D: Transmembrane protein, putative
E: DNA (27-MER)
F: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,9247
Polymers174,5256
Non-polymers3981
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein mRNA m(6)A methyltransferase


Mass: 43368.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote)
Gene: TTHERM_00704040 / Production host: Escherichia coli (E. coli) / References: UniProt: Q22GC0, mRNA m6A methyltransferase
#2: Protein MT-a70 family protein MTA9


Mass: 55576.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote)
Gene: TTHERM_00301770 / Production host: Escherichia coli (E. coli) / References: UniProt: I7MIF9
#3: Protein Myb-like DNA-binding domain protein


Mass: 41937.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote)
Gene: TTHERM_00161750 / Production host: Escherichia coli (E. coli) / References: UniProt: Q22VV9
#4: Protein Transmembrane protein, putative


Mass: 17043.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote)
Gene: TTHERM_00439330 / Production host: Escherichia coli (E. coli) / References: UniProt: I7M8B9

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DNA chain , 2 types, 2 molecules EF

#5: DNA chain DNA (27-MER)


Mass: 8426.495 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#6: DNA chain DNA (27-MER)


Mass: 8173.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 1 types, 1 molecules

#7: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tetrahymena MTA1c with hmDNA and SAM / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Details: 20 mM HEPES pH 7.5, 50 mM K glutamate, 0.5 mM TCEP, 0.025% beta-OG
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 13000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 6718
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2PHENIX1.21.1_5286+SVNmodel refinement
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 203776 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 70 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00387817
ELECTRON MICROSCOPYf_angle_d0.679710709
ELECTRON MICROSCOPYf_chiral_restr0.04321164
ELECTRON MICROSCOPYf_plane_restr0.00471203
ELECTRON MICROSCOPYf_dihedral_angle_d21.70431426

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