+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17329 | |||||||||
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Title | 48S late-stage initiation complex with m6A mRNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | translation initiation / ribosome / m6A / methylated mRNA / TRANSLATION | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.04 Å | |||||||||
Authors | Guca E / Lima LHF / Boissier F / Hashem Y | |||||||||
Funding support | European Union, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17329.map.gz | 173.2 MB | EMDB map data format | |
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Header (meta data) | emd-17329-v30.xml emd-17329.xml | 56.2 KB 56.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17329_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_17329.png | 32.1 KB | ||
Filedesc metadata | emd-17329.cif.gz | 12.4 KB | ||
Others | emd_17329_additional_1.map.gz emd_17329_half_map_1.map.gz emd_17329_half_map_2.map.gz | 190.7 MB 171.2 MB 171.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17329 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17329 | HTTPS FTP |
-Related structure data
Related structure data | 8p03MC 8p09C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17329.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_17329_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17329_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17329_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 48S late-stage initiation complex with m6A-modified mRNA
+Supramolecule #1: 48S late-stage initiation complex with m6A-modified mRNA
+Macromolecule #1: initiator methionylated tRNA
+Macromolecule #2: 18S ribosomal RNA
+Macromolecule #3: m6A-methylated mRNA
+Macromolecule #4: Eukaryotic translation initiation factor 2 subunit 1
+Macromolecule #5: 40S ribosomal protein SA
+Macromolecule #6: ribosomal protein eS1
+Macromolecule #7: 40S ribosomal protein S2
+Macromolecule #8: Ribosomal protein S3
+Macromolecule #9: 40S ribosomal protein S4
+Macromolecule #10: Ribosomal protein S5
+Macromolecule #11: 40S ribosomal protein S6
+Macromolecule #12: ribosomal protein eS7
+Macromolecule #13: 40S ribosomal protein S8
+Macromolecule #14: 40S ribosomal protein S9
+Macromolecule #15: 40S ribosomal protein eS10
+Macromolecule #16: 40S ribosomal protein S11
+Macromolecule #17: 40S ribosomal protein S12
+Macromolecule #18: ribosomal protein uS15
+Macromolecule #19: 40S ribosomal protein uS11
+Macromolecule #20: 40S ribosomal protein uS19
+Macromolecule #21: 40S ribosomal protein uS9
+Macromolecule #22: 40S ribosomal protein eS17
+Macromolecule #23: 40S ribosomal protein uS13
+Macromolecule #24: 40S ribosomal protein eS19
+Macromolecule #25: 40S ribosomal protein uS10
+Macromolecule #26: 40S ribosomal protein S21
+Macromolecule #27: Ribosomal protein S15a
+Macromolecule #28: 40S ribosomal protein S23
+Macromolecule #29: 40S ribosomal protein S24
+Macromolecule #30: 40S ribosomal protein S26
+Macromolecule #31: 40S ribosomal protein S27
+Macromolecule #32: 40S ribosomal protein S28
+Macromolecule #33: 40S ribosomal protein S29
+Macromolecule #34: ribosomal protein eS31
+Macromolecule #35: Ribosomal protein RACK1
+Macromolecule #36: 40S ribosomal protein S30
+Macromolecule #37: Eukaryotic translation initiation factor 4C
+Macromolecule #38: ATP binding cassette subfamily E member 1
+Macromolecule #39: 60S ribosomal protein L41
+Macromolecule #40: 40S ribosomal protein S25
+Macromolecule #41: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.3 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |