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- EMDB-4049: Ribosomal 18S rRNA base pairs with mRNA during eukaryotic transla... -

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Basic information

Entry
Database: EMDB / ID: EMD-4049
TitleRibosomal 18S rRNA base pairs with mRNA during eukaryotic translation initiation
Map data
Sample
  • Complex: Rabbit reticulocyte 80S ribosome assembled on histone H4 mRNA
    • Complex: h4-mRNA, P-tRNA, A/T state tRNA, eEF1A
Methodsingle particle reconstruction / cryo EM / Resolution: 10.2 Å
AuthorsMartin F / Menetret J-F / Simonetti A / Myasniko AG / Vicens Q / Prongidi-Fix L / Natchiar SK / Klaholz BP / Eriani G
CitationJournal: 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
DepositionJul 13, 2016-
Header (metadata) releaseSep 7, 2016-
Map releaseSep 7, 2016-
UpdateSep 7, 2016-
Current statusSep 7, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4049.png

Downloads & links

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Map

FileDownload / File: emd_4049.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel size
XYZ
EMDB info.1.11.11.1
CCP4 map header1.11.11.1
EM Navigator Movie #12.22.22.2
Density
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.007
Minimum - Maximum-0.05037985 - 0.07009276
Average (Standard dev.)0.00016077438 (±0.0045864847)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 246.40001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z246.400246.400246.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.0500.0700.000

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Supplemental data

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Sample components

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Entire : Rabbit reticulocyte 80S ribosome assembled on histone H4 mRNA

EntireName: Rabbit reticulocyte 80S ribosome assembled on histone H4 mRNA
Components
  • Complex: Rabbit reticulocyte 80S ribosome assembled on histone H4 mRNA
    • Complex: h4-mRNA, P-tRNA, A/T state tRNA, eEF1A

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Supramolecule #1: Rabbit reticulocyte 80S ribosome assembled on histone H4 mRNA

SupramoleculeName: 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

SupramoleculeName: h4-mRNA, P-tRNA, A/T state tRNA, eEF1A / type: complex / ID: 2 / Parent: 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 95 %
Details0.2-0.5 mg/ml

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION
Image recordingFilm 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

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Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionNumber classes used: 5 / Resolution.type: BY AUTHOR / Resolution: 10.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146821

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