+Open data
-Basic information
Entry | Database: PDB / ID: 7yi8 | ||||||
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Title | Cryo-EM structure of SAH-bound MTA1-MTA9-p1-p2 complex | ||||||
Components |
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Keywords | DNA 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 | ||||||
Biological species | Tetrahymena thermophila SB210 (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||
Authors | Yan, J.J. / Guan, Z.Y. / Liu, F.Q. / Yan, X.H. / Hou, M.J. / Yin, P. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yi8.cif.gz | 143.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yi8.ent.gz | 101.3 KB | Display | PDB format |
PDBx/mmJSON format | 7yi8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yi8_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7yi8_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7yi8_validation.xml.gz | 30.3 KB | Display | |
Data in CIF | 7yi8_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/7yi8 ftp://data.pdbj.org/pub/pdb/validation_reports/yi/7yi8 | HTTPS FTP |
-Related structure data
Related structure data | 33853MC 7yi9C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 / Gene: TTHERM_00301770 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7MIF9 |
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#2: Protein | 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 | 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 | 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-SAH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: MTAc holoenzyme / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: Tetrahymena thermophila SB210 (eukaryote) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 54 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: cryoSPARC / Category: final Euler assignment | ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 614753 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.31 Å2 | ||||||||||||||||||||||||
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