+Open data
-Basic information
Entry | Database: PDB / ID: 8p03 | ||||||
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Title | 48S late-stage initiation complex with m6A mRNA | ||||||
Components |
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Keywords | TRANSLATION / translation initiation / ribosome / m6A / methylated mRNA | ||||||
Function / homology | Function and homology information Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) ...Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal subunit / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rough endoplasmic reticulum / regulation of translational fidelity / translation initiation factor activity / DNA-(apurinic or apyrimidinic site) lyase / small-subunit processome / ribosomal small subunit biogenesis / cytoplasmic stress granule / cytosolic small ribosomal subunit / cytoplasmic translation / cell differentiation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / synapse / nucleolus / ATP hydrolysis activity / RNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å | ||||||
Authors | Guca, E. / Lima, L.H.F. / Boissier, F. / Hashem, Y. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Mol Cell / Year: 2024 Title: N-methyladenosine in 5' UTR does not promote translation initiation. Authors: Ewelina Guca / Rodrigo Alarcon / Michael Z Palo / Leonardo Santos / Santiago Alonso-Gil / Marcos Davyt / Leonardo H F de Lima / Fanny Boissier / Sarada Das / Bojan Zagrovic / Joseph D ...Authors: Ewelina Guca / Rodrigo Alarcon / Michael Z Palo / Leonardo Santos / Santiago Alonso-Gil / Marcos Davyt / Leonardo H F de Lima / Fanny Boissier / Sarada Das / Bojan Zagrovic / Joseph D Puglisi / Yaser Hashem / Zoya Ignatova / Abstract: The most abundant N-methyladenosine (mA) modification on mRNAs is installed non-stoichiometrically across transcripts, with 5' untranslated regions (5' UTRs) being the least conductive. 5' UTRs are ...The most abundant N-methyladenosine (mA) modification on mRNAs is installed non-stoichiometrically across transcripts, with 5' untranslated regions (5' UTRs) being the least conductive. 5' UTRs are essential for translation initiation, yet the molecular mechanisms orchestrated by mA remain poorly understood. Here, we combined structural, biochemical, and single-molecule approaches and show that at the most common position, a single mA does not affect translation yields, the kinetics of translation initiation complex assembly, or start codon recognition both under permissive growth and following exposure to oxidative stress. Cryoelectron microscopy (cryo-EM) structures of the late preinitiation complex reveal that mA purine ring established stacking interactions with an arginine side chain of the initiation factor eIF2α, although with only a marginal energy contribution, as estimated computationally. These findings provide molecular insights into mA interactions with the initiation complex and suggest that the subtle stabilization is unlikely to affect the translation dynamics under homeostatic conditions or stress. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p03.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8p03.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 8p03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/8p03 ftp://data.pdbj.org/pub/pdb/validation_reports/p0/8p03 | HTTPS FTP |
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-Related structure data
Related structure data | 17329MC 8p09C 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
-RNA chain , 3 types, 3 molecules 123
#1: RNA chain | Mass: 24376.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
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#2: RNA chain | Mass: 601015.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#3: RNA chain | Mass: 2882.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit) |
-Eukaryotic translation initiation factor ... , 2 types, 2 molecules Aj
#4: Protein | Mass: 32792.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T2G4 |
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#37: Protein | Mass: 12788.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYS4 |
+40S ribosomal protein ... , 25 types, 25 molecules CEGIKLMNOQRSTUVWXZabcdein
-Ribosomal protein ... , 8 types, 8 molecules DFHJPYfg
#6: Protein | Mass: 24944.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN72 |
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#8: Protein | Mass: 25158.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) References: UniProt: G1TNM3, DNA-(apurinic or apyrimidinic site) lyase |
#10: Protein | Mass: 21525.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KMN4 |
#12: Protein | Mass: 21716.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0 |
#18: Protein | Mass: 17128.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51 |
#27: Protein | Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89 |
#34: Protein | Mass: 8358.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22 |
#35: Protein | Mass: 34669.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4 |
-Protein / Protein/peptide / Non-polymers , 3 types, 180 molecules kl
#38: Protein | Mass: 66986.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SG72 |
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#39: Protein/peptide | Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4 |
#41: Chemical | ChemComp-MG / |
-Details
Has ligand of interest | N |
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-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: 48S late-stage initiation complex with m6A-modified mRNA Type: RIBOSOME / Entity ID: #1-#40 / Source: NATURAL |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: OTHER / Nominal defocus max: 2300 nm / Nominal defocus min: 300 nm |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103050 / Symmetry type: POINT |