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- EMDB-1185: Interactions of the release factor RF1 with the ribosome as revea... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1185 | |||||||||
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Title | Interactions of the release factor RF1 with the ribosome as revealed by cryo-EM. | |||||||||
![]() | This is an EM map of a 70s E.coli ribosome | |||||||||
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Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 14.0 Å | |||||||||
![]() | Rawat U / Gao H / Zavialov A / Gursky R / Ehrenberg M / Frank J | |||||||||
![]() | ![]() Title: Interactions of the release factor RF1 with the ribosome as revealed by cryo-EM. Authors: Urmila Rawat / Haixiao Gao / Andrey Zavialov / Richard Gursky / Måns Ehrenberg / Joachim Frank / ![]() Abstract: In eubacteria, termination of translation is signaled by any one of the stop codons UAA, UAG, and UGA moving into the ribosomal A site. Two release factors, RF1 and RF2, recognize and bind to the ...In eubacteria, termination of translation is signaled by any one of the stop codons UAA, UAG, and UGA moving into the ribosomal A site. Two release factors, RF1 and RF2, recognize and bind to the stop codons with different affinities and trigger the hydrolysis of the ester bond that links the polypeptide with the P-site tRNA. Cryo-electron microscopy (cryo-EM) results obtained in this study show that ribosome-bound RF1 is in an open conformation, unlike the closed conformation observed in the crystal structure of the free factor, allowing its simultaneous access to both the decoding center and the peptidyl-transferase center. These results are similar to those obtained for RF2, but there is an important difference in how the factors bind to protein L11, which forms part of the GTPase-associated center of the large ribosomal subunit. The difference in the binding position, C-terminal domain for RF2 versus N-terminal domain for RF1, explains a body of L11 mutation studies that revealed differential effects on the activity of the two factors. Very recent data obtained with small-angle X-ray scattering now reveal that the solution structure of RF1 is open, as here seen on the ribosome by cryo-EM, and not closed, as seen in the crystal. | |||||||||
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 | ![]() | 7.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.5 KB 11.5 KB | Display Display | ![]() |
Images | ![]() | 10.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fvoMC ![]() 1184C 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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is an EM map of a 70s E.coli ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.82 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 : GAQ mutant
Entire | Name: GAQ mutant |
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Components |
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-Supramolecule #1000: GAQ mutant
Supramolecule | Name: GAQ mutant / type: sample / ID: 1000 / Number unique components: 6 |
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-Supramolecule #1: 30S
Supramolecule | Name: 30S / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: SSU 30S |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #2: 50S
Supramolecule | Name: 50S / type: complex / ID: 2 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: LSU 50S |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: P-site tRNA
Macromolecule | Name: P-site tRNA / type: rna / ID: 1 / Classification: OTHER / Structure: OTHER / Synthetic?: No |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #2: E-site tRNA
Macromolecule | Name: E-site tRNA / type: rna / ID: 2 / Classification: OTHER / Structure: OTHER / Synthetic?: No |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #3: mRNA
Macromolecule | Name: mRNA / type: rna / ID: 3 / Classification: OTHER / Structure: DOUBLE HELIX / Synthetic?: Yes |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #4: RF1
Macromolecule | Name: RF1 / type: protein_or_peptide / ID: 4 / Recombinant expression: No |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 93 K / Instrument: HOMEMADE PLUNGER Details: Vitrification instrument: two sided blotting plunger Method: Blot for 2 seconds before plunging |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 93 K |
Alignment procedure | Legacy - Electron beam tilt params: 0 |
Date | Dec 1, 2002 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 56 / Average electron dose: 20 e/Å2 / Od range: 1.2 / Bits/pixel: 12 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 49696 / 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: 50000 |
Sample stage | Specimen holder: Cryo stage / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: defocus groups |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, package / Number images used: 13157 |
Final angle assignment | Details: SPIDER: theta 15 degrees, phi 15 degrees |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: O |
Details | Protocol: Rigid Body. manual fitting in O |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient |
Output model | ![]() PDB-2fvo: |