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- PDB-8xyp: Cryo-EM structure of SAH-bound Tetrahymena DNA methyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 8xyp
TitleCryo-EM structure of SAH-bound Tetrahymena DNA methyltransferase complex MTA1c
Components
  • MT-a70 family protein
  • Methyltransferase MT, putative
  • Myb-like DNA-binding domain protein
  • Transmembrane protein, putative
KeywordsDNA BINDING PROTEIN / DNA methyltransferase / DNA N6-methyladenine modification / chromatin regulation / gene regulation
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
S-ADENOSYL-L-HOMOCYSTEINE / Transmembrane protein, putative / mRNA m(6)A methyltransferase / Myb-like domain-containing protein / Methyltransferase MT, putative
Similarity search - Component
Biological speciesTetrahymena thermophila SB210 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsXu, Q. / Shi, Z.B.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MT-a70 family protein
B: Methyltransferase MT, putative
C: Myb-like DNA-binding domain protein
D: Transmembrane protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,0045
Polymers143,6194
Non-polymers3841
Water00
1


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

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Components

#1: Protein MT-a70 family protein


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
#2: Protein Methyltransferase MT, putative


Mass: 41269.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote)
Gene: TTHERM_01005150 / Production host: Escherichia coli (E. coli) / References: UniProt: Q22XT1
#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
#5: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
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 SAH / Type: COMPLEX / Entity ID: #1-#4 / 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, 0.05% 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: 130000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 48 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of real images: 3634
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameCategory
1Topazparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 372998 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / 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: 52.45 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00365419
ELECTRON MICROSCOPYf_angle_d0.59987278
ELECTRON MICROSCOPYf_chiral_restr0.0465772
ELECTRON MICROSCOPYf_plane_restr0.0044934
ELECTRON MICROSCOPYf_dihedral_angle_d5.4331707

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