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Yorodumi- EMDB-4049: Ribosomal 18S rRNA base pairs with mRNA during eukaryotic transla... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4049 | |||||||||
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Title | Ribosomal 18S rRNA base pairs with mRNA during eukaryotic translation initiation | |||||||||
Map data | ||||||||||
Sample |
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Method | single particle reconstruction / cryo EM / Resolution: 10.2 Å | |||||||||
Authors | Martin F / Menetret J-F / Simonetti A / Myasniko AG / Vicens Q / Prongidi-Fix L / Natchiar SK / Klaholz BP / Eriani G | |||||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Ribosomal 18S rRNA base pairs with mRNA during eukaryotic translation initiation. Authors: Franck Martin / Jean-François Ménétret / Angelita Simonetti / Alexander G Myasnikov / Quentin Vicens / Lydia Prongidi-Fix / S Kundhavai Natchiar / Bruno P Klaholz / Gilbert Eriani / Abstract: Eukaryotic mRNAs often contain a Kozak sequence that helps tether the ribosome to the AUG start codon. The mRNA of histone H4 (h4) does not undergo classical ribosome scanning but has evolved a ...Eukaryotic mRNAs often contain a Kozak sequence that helps tether the ribosome to the AUG start codon. The mRNA of histone H4 (h4) does not undergo classical ribosome scanning but has evolved a specific tethering mechanism. The cryo-EM structure of the rabbit ribosome complex with mouse h4 shows that the mRNA forms a folded, repressive structure at the mRNA entry site on the 40S subunit next to the tip of helix 16 of 18S ribosomal RNA (rRNA). Toe-printing and mutational assays reveal that an interaction exists between a purine-rich sequence in h4 mRNA and a complementary UUUC sequence of helix h16. Together the present data establish that the h4 mRNA harbours a sequence complementary to an 18S rRNA sequence which tethers the mRNA to the ribosome to promote proper start codon positioning, complementing the interactions of the 40S subunit with the Kozak sequence that flanks the AUG start codon. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4049.map.gz | 33.2 MB | EMDB map data format | |
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Header (meta data) | emd-4049-v30.xml emd-4049.xml | 8 KB 8 KB | Display Display | EMDB header |
Images | emd_4049.png | 145.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4049 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4049 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4049.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size |
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Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Rabbit reticulocyte 80S ribosome assembled on histone H4 mRNA
Entire | Name: Rabbit reticulocyte 80S ribosome assembled on histone H4 mRNA |
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Components |
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-Supramolecule #1: Rabbit reticulocyte 80S ribosome assembled on histone H4 mRNA
Supramolecule | Name: Rabbit reticulocyte 80S ribosome assembled on histone H4 mRNA type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: 80S,h4-mRNA, P-tRNA, A/T-tRNA,eEF1A |
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-Supramolecule #2: h4-mRNA, P-tRNA, A/T state tRNA, eEF1A
Supramolecule | Name: h4-mRNA, P-tRNA, A/T state tRNA, eEF1A / type: complex / ID: 2 / Parent: 1 |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % |
Details | 0.2-0.5 mg/ml |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: DIFFRACTION |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: OTHER / Average electron dose: 3.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: NOT APPLICABLE |
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Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Number classes used: 5 / Resolution.type: BY AUTHOR / Resolution: 10.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146821 |