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- EMDB-2790: The molecular structure of the left-handed supra- molecular helix... -

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Basic information

Entry
Database: EMDB / ID: EMD-2790
TitleThe molecular structure of the left-handed supra- molecular helix of eukaryotic polyribosomes
Map data3D poly-ribosome structure from Wheat Germ in vitro cell free system
Sample
  • Sample: poly-ribosome from in vitro wheat germ system
  • Complex: Wheat germ poly-ribosome
Keywordscryo-ET / polyribosome / sub-tomogram averaging
Function / homology
Function and homology information


cytoplasmic translational elongation / protein kinase activator activity / translational elongation / ribonucleoprotein complex binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / ribosome biogenesis / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...cytoplasmic translational elongation / protein kinase activator activity / translational elongation / ribonucleoprotein complex binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / ribosome biogenesis / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / ribosome / structural constituent of ribosome / G protein-coupled receptor signaling pathway / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Ribosomal protein P2 / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / 60s Acidic ribosomal protein / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L18e / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. ...Ribosomal protein P2 / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / 60s Acidic ribosomal protein / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L18e / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L19, eukaryotic / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / : / Ribosomal protein L30e signature 1. / Ribosomal protein L6e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L36e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / Ribosomal protein L30/YlxQ / Ribosomal Protein L6, KOW domain / Ribosomal protein L13, eukaryotic/archaeal / 60S ribosomal protein L35 / Ribosomal protein L6e / 60S ribosomal protein L6E / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein L7, eukaryotic / Ribosomal_L19e / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L37ae/L37e / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L7/L30 / : / Ribosomal protein S14/S29 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / K homology domain superfamily, prokaryotic type / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein L13 signature. / Ribosomal protein S14 / Ribosomal protein L13, conserved site / Ribosomal protein S14p/S29e / K homology domain-like, alpha/beta / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain
Similarity search - Domain/homology
60S ribosomal protein L37a, expressed / Small ribosomal subunit protein uS14 / Ribosomal protein L17 / Ribosomal protein P1 / Ribosomal protein L7 / Ribosomal protein L39 / Ribosomal protein l34 / Large ribosomal subunit protein eL30 / Ribosomal protein L18 / Ribosomal protein L13a ...60S ribosomal protein L37a, expressed / Small ribosomal subunit protein uS14 / Ribosomal protein L17 / Ribosomal protein P1 / Ribosomal protein L7 / Ribosomal protein L39 / Ribosomal protein l34 / Large ribosomal subunit protein eL30 / Ribosomal protein L18 / Ribosomal protein L13a / Ribosomal protein L11 / Ribosomal protein / 60S ribosomal protein L6 / 60S ribosomal protein L36 / Ribosomal protein L3 / Ribosomal Pr 117 / Ribosomal protein L19 / 30S ribosomal protein S3, chloroplastic / Large ribosomal subunit protein uL29 / G protein beta subunit / Uncharacterized protein / :
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
Methodsubtomogram averaging / cryo EM / Resolution: 34.0 Å
AuthorsMyasnikov AG / Afonina ZHA / Menetret J-F / Shirokov VA / Spirin AS / Klaholz BP
CitationJournal: Nat Commun / Year: 2014
Title: The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes.
Authors: Alexander G Myasnikov / Zhanna A Afonina / Jean-François Ménétret / Vladimir A Shirokov / Alexander S Spirin / Bruno P Klaholz /
Abstract: During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a ...During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a 100 MDa eukaryotic poly-ribosome complex derived from cryo electron tomography, sub-tomogram averaging and pseudo-atomic modelling by crystal structure fitting. The structure allowed the visualization of the three functional parts of the polysome assembly, the central core region that forms a rather compact left-handed supra-molecular helix, and the more open regions that harbour the initiation and termination sites at either ends. The helical region forms a continuous mRNA channel where the mRNA strand bridges neighbouring exit and entry sites of the ribosomes and prevents mRNA looping between ribosomes. This structure provides unprecedented insights into protein- and RNA-mediated inter-ribosome contacts that involve conserved sites through 40S subunits and long protruding RNA expansion segments, suggesting a role in stabilizing the overall polyribosomal assembly.
History
DepositionOct 3, 2014-
Header (metadata) releaseNov 19, 2014-
Map releaseNov 26, 2014-
UpdateJul 15, 2015-
Current statusJul 15, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4v3p
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4v3p
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2790.png

Downloads & links

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Map

FileDownload / File: emd_2790.map.gz / Format: CCP4 / Size: 48.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D poly-ribosome structure from Wheat Germ in vitro cell free system
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.8 Å/pix.
x 200 pix.
= 1360. Å		6.8 Å/pix.
x 256 pix.
= 1740.8 Å		6.8 Å/pix.
x 256 pix.
= 1740.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 6.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-14.011762620000001 - 16.279329300000001
Average (Standard dev.)0.0 (±1.00000012)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-100
Dimensions256256200
Spacing256256200
CellA: 1740.8 Å / B: 1740.8 Å / C: 1360.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.86.86.8
M x/y/z256256200
origin x/y/z0.0000.0000.000
length x/y/z1740.8001740.8001360.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS-128-128-100
NC/NR/NS256256200
D min/max/mean-14.01216.279-0.000

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Supplemental data

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Sample components

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Entire : poly-ribosome from in vitro wheat germ system

EntireName: poly-ribosome from in vitro wheat germ system
Components
  • Sample: poly-ribosome from in vitro wheat germ system
  • Complex: Wheat germ poly-ribosome

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Supramolecule #1000: poly-ribosome from in vitro wheat germ system

SupramoleculeName: poly-ribosome from in vitro wheat germ system / type: sample / ID: 1000 / Oligomeric state: 23-meric / Number unique components: 1
Molecular weightTheoretical: 100 MDa

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Supramolecule #1: Wheat germ poly-ribosome

SupramoleculeName: Wheat germ poly-ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Triticum aestivum (bread wheat) / synonym: Wheat Germ / Tissue: Germ
Molecular weightTheoretical: 100 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statehelical array

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.6
Details: 25mM HEPES-KOH, 3mM Mg(OAc)2, 85mM KOAc, 1.6mM DTT, 0.25mM spermidine
GridDetails: 3ul of sample applied on 300 mesh holy carbon Quantifoil 2/2 grid. Blotting was done in Vitrobot Mark IV
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV
Method: 3ul of sample applied on 300 mesh holy carbon Quantifoil 2/2 grid. Blotting was done in Vitrobot Mark IV, blot time 0.5 sec, blot force 5

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Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureMin: 80 K / Max: 100 K / Average: 90 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification
Legacy - Electron beam tilt params: 0
DateJan 1, 2013
Image recordingCategory: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Average electron dose: 30 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 150 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 41176 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 39000
Sample stageSpecimen holder model: GATAN HELIUM / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 70 °
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

DetailsThe subtomograms were selected in imod manually. The averaging was done in xmipp program by using ml_tomo subroutine.
Final reconstructionApplied symmetry - Helical parameters - Δz: 83 Å
Applied symmetry - Helical parameters - Δ&Phi: 90 °
Applied symmetry - Helical parameters - Axial symmetry: C4 (4 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: OTHER / Software - Name: Imod, Xmipp, Imagic / Number subtomograms used: 106
Final 3D classificationNumber classes: 1

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Atomic model buiding 1

Initial modelPDB ID:

3iz6
PDB Unreleased entry

SoftwareName: Chimera
Details40S and 60S was fitted separately
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4v3p:
The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes

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Atomic model buiding 2

Initial modelPDB ID:

3iz7
PDB Unreleased entry

SoftwareName: Chimera
Details40S and 60S was fitted separately
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4v3p:
The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes

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Atomic model buiding 3

Initial modelPDB ID:

3izr
PDB Unreleased entry

SoftwareName: Chimera
Details40S and 60S was fitted separately
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4v3p:
The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes

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Atomic model buiding 4

Initial modelPDB ID:

3iz9
PDB Unreleased entry

SoftwareName: Chimera
Details40S and 60S was fitted separately
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4v3p:
The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes

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