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- PDB-9o6k: Cryo-EM structure of AMT1-AMT7-AMTP1-AMTP2 complex -

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Basic information

Entry
Database: PDB / ID: 9o6k
TitleCryo-EM structure of AMT1-AMT7-AMTP1-AMTP2 complex
Components
  • AMT7
  • AMTP2
  • Myb-like domain-containing protein
  • mRNA m(6)A methyltransferase
KeywordsTRANSFERASE / 6mA methyltransferase
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-ADENOSYL-L-HOMOCYSTEINE / Transmembrane protein, putative / Uncharacterized protein / mRNA m(6)A methyltransferase / Myb-like domain-containing protein
Similarity search - Component
Biological speciesTetrahymena thermophila SB210 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsSong, J. / Shao, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of AMT1-AMT7-AMTP1-AMTP2 complex
Authors: Song, J. / Shao, Z.
History
DepositionApr 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 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

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Assembly

Deposited unit
A: AMT7
B: mRNA m(6)A methyltransferase
C: Myb-like domain-containing protein
H: AMTP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,3805
Polymers152,9954
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 AMT7


Mass: 52083.430 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 BL21(DE3) (bacteria) / References: UniProt: I7MIF9
#2: Protein mRNA m(6)A methyltransferase


Mass: 42696.059 Da / Num. of mol.: 1 / Fragment: UNP residues 57-428
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote)
Gene: TTHERM_00704040 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q22GC0, mRNA m6A methyltransferase
#3: Protein Myb-like domain-containing protein / AMTP1


Mass: 41602.758 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 BL21(DE3) (bacteria) / References: UniProt: Q22VV9
#4: Protein AMTP2


Mass: 16612.893 Da / Num. of mol.: 1 / Fragment: UNP residues 154-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote)
Gene: TTHERM_00439330 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: AMT1-AMT7-AMTP1-AMTP2 complex / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 3100 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 53.55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66922 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036193
ELECTRON MICROSCOPYf_angle_d0.6628331
ELECTRON MICROSCOPYf_dihedral_angle_d5.181803
ELECTRON MICROSCOPYf_chiral_restr0.043912
ELECTRON MICROSCOPYf_plane_restr0.0041066

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