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- PDB-7yi9: Cryo-EM structure of SAM-bound MTA1-MTA9-p1-p2 complex -

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Basic information

Entry
Database: PDB / ID: 7yi9
TitleCryo-EM structure of SAM-bound MTA1-MTA9-p1-p2 complex
Components
  • MT-a70 family protein
  • MTA9
  • P1
  • Transmembrane protein, putative
KeywordsDNA BINDING PROTEIN / N6-adenine methylation / MTAc holoenzyme
Function / homology
Function and homology information


RNA N6-methyladenosine methyltransferase complex / : / methyltransferase activity / membrane / nucleus
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 / Transmembrane protein, putative / Uncharacterized protein / MT-a70 family protein / Myb-like domain-containing protein
Similarity search - Component
Biological speciesTetrahymena thermophila SB210 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsYan, J.J. / Guan, Z.Y. / Liu, F.Q. / Yan, X.H. / Hou, M.J. / Yin, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2023
Title: Structural insights into DNA N-adenine methylation by the MTA1 complex.
Authors: Junjun Yan / Feiqing Liu / Zeyuan Guan / Xuhui Yan / Xiaohuan Jin / Qiang Wang / Zican Wang / Junjie Yan / Delin Zhang / Zhu Liu / Shan Wu / Ping Yin /
Abstract: N-methyldeoxyadenine (6mA) has recently been reported as a prevalent DNA modification in eukaryotes. The Tetrahymena thermophila MTA1 complex consisting of four subunits, namely MTA1, MTA9, p1, and ...N-methyldeoxyadenine (6mA) has recently been reported as a prevalent DNA modification in eukaryotes. The Tetrahymena thermophila MTA1 complex consisting of four subunits, namely MTA1, MTA9, p1, and p2, is the first identified eukaryotic 6mA methyltransferase (MTase) complex. Unlike the prokaryotic 6mA MTases which have been biochemically and structurally characterized, the operation mode of the MTA1 complex remains largely elusive. Here, we report the cryogenic electron microscopy structures of the quaternary MTA1 complex in S-adenosyl methionine (SAM)-bound (2.6 Å) and S-adenosyl homocysteine (SAH)-bound (2.8 Å) states. Using an AI-empowered integrative approach based on AlphaFold prediction and chemical cross-linking mass spectrometry, we further modeled a near-complete structure of the quaternary complex. Coupled with biochemical characterization, we revealed that MTA1 serves as the catalytic core, MTA1, MTA9, and p1 likely accommodate the substrate DNA, and p2 may facilitate the stabilization of MTA1. These results together offer insights into the molecular mechanism underpinning methylation by the MTA1 complex and the potential diversification of MTases for N-adenine methylation.
History
DepositionJul 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MTA9
B: MT-a70 family protein
C: P1
D: Transmembrane protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,6105
Polymers156,2124
Non-polymers3981
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein MTA9


Mass: 52026.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote)
Strain: SB210 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7MIF9
#2: Protein MT-a70 family protein / MTA1


Mass: 42696.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote)
Strain: SB210 / Gene: TTHERM_00704040 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q22GC0
#3: Protein P1


Mass: 41602.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote)
Strain: SB210 / Gene: TTHERM_00161750 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q22VV9
#4: Protein Transmembrane protein, putative / P2


Mass: 19886.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote)
Strain: SB210 / Gene: TTHERM_00439330 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7M8B9
#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


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

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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: MTAc holoenzyme / 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: 8
SpecimenConc.: 0.25 mg/ml / Embedding 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
EM software
IDNameCategory
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
CTF correctionType: NONE
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 628049 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035319
ELECTRON MICROSCOPYf_angle_d0.5727149
ELECTRON MICROSCOPYf_dihedral_angle_d5.965688
ELECTRON MICROSCOPYf_chiral_restr0.044780
ELECTRON MICROSCOPYf_plane_restr0.004909

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