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- EMDB-2790: The molecular structure of the left-handed supra- molecular helix... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2790 | |||||||||
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Title | The molecular structure of the left-handed supra- molecular helix of eukaryotic polyribosomes | |||||||||
![]() | 3D poly-ribosome structure from Wheat Germ in vitro cell free system | |||||||||
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![]() | cryo-ET / polyribosome / sub-tomogram averaging | |||||||||
Function / homology | ![]() translational elongation / protein kinase activator activity / ribonucleoprotein complex binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation ...translational elongation / protein kinase activator activity / ribonucleoprotein complex binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / signal transduction / RNA binding / zinc ion binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 34.0 Å | |||||||||
![]() | Myasnikov AG / Afonina ZHA / Menetret J-F / Shirokov VA / Spirin AS / Klaholz BP | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 32.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.9 KB 12.9 KB | Display Display | ![]() |
Images | ![]() | 70.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 191.6 KB | Display | ![]() |
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Full document | ![]() | 190.7 KB | Display | |
Data in XML | ![]() | 4.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4v3pMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | 3D poly-ribosome structure from Wheat Germ in vitro cell free system | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : poly-ribosome from in vitro wheat germ system
Entire | Name: poly-ribosome from in vitro wheat germ system |
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Components |
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-Supramolecule #1000: poly-ribosome from in vitro wheat germ system
Supramolecule | Name: poly-ribosome from in vitro wheat germ system / type: sample / ID: 1000 / Oligomeric state: 23-meric / Number unique components: 1 |
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Molecular weight | Theoretical: 100 MDa |
-Supramolecule #1: Wheat germ poly-ribosome
Supramolecule | Name: Wheat germ poly-ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 100 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | helical array |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.6 Details: 25mM HEPES-KOH, 3mM Mg(OAc)2, 85mM KOAc, 1.6mM DTT, 0.25mM spermidine |
Grid | Details: 3ul of sample applied on 300 mesh holy carbon Quantifoil 2/2 grid. Blotting was done in Vitrobot Mark IV |
Vitrification | Cryogen 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
Microscope | FEI TECNAI F30 |
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Temperature | Min: 80 K / Max: 100 K / Average: 90 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification Legacy - Electron beam tilt params: 0 |
Date | Jan 1, 2013 |
Image recording | Category: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Average electron dose: 30 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 150 kV / Electron source: ![]() |
Electron optics | Calibrated 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 stage | Specimen 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
Details | The subtomograms were selected in imod manually. The averaging was done in xmipp program by using ml_tomo subroutine. |
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Final reconstruction | Applied 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 classification | Number classes: 1 |
-Atomic model buiding 1
Initial model | PDB ID: ![]() 3iz6 |
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Software | Name: ![]() |
Details | 40S and 60S was fitted separately |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-4v3p: |
-Atomic model buiding 2
Initial model | PDB ID: ![]() 3iz7 |
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Software | Name: ![]() |
Details | 40S and 60S was fitted separately |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-4v3p: |
-Atomic model buiding 3
Initial model | PDB ID: ![]() 3izr |
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Software | Name: ![]() |
Details | 40S and 60S was fitted separately |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-4v3p: |