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Yorodumi- EMDB-1064: Visualization of release factor 3 on the ribosome during terminat... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1064 | |||||||||
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Title | Visualization of release factor 3 on the ribosome during termination of protein synthesis. | |||||||||
Map data | Cryo-EM map of the E.coli 70S/RF3 complex, state 1 | |||||||||
Sample |
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Function / homology | Peptide chain release factor 3 Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 17.9 Å | |||||||||
Authors | Klaholz BP | |||||||||
Citation | Journal: Nature / Year: 2004 Title: Visualization of release factor 3 on the ribosome during termination of protein synthesis. Authors: Bruno P Klaholz / Alexander G Myasnikov / Marin Van Heel / Abstract: Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the ribosome after release of the ...Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the ribosome after release of the nascent polypeptide. RF3 in the GDP state binds to the ribosomal class I RF complex, followed by an exchange of GDP for GTP and release of the class I RF. As GTP hydrolysis triggers release of RF3 (ref. 4), we trapped RF3 on Escherichia coli ribosomes using a nonhydrolysable GTP analogue. Here we show by cryo-electron microscopy that the complex can adopt two different conformational states. In 'state 1', RF3 is pre-bound to the ribosome, whereas in 'state 2' RF3 contacts the ribosome GTPase centre. The transfer RNA molecule translocates from the peptidyl site in state 1 to the exit site in state 2. This translocation is associated with a large conformational rearrangement of the ribosome. Because state 1 seems able to accommodate simultaneously both RF3 and RF2, whose position is known from previous studies, we can infer the release mechanism of class I RFs. | |||||||||
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_1064.map.gz | 2.7 MB | EMDB map data format | |
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Header (meta data) | emd-1064-v30.xml emd-1064.xml | 10.8 KB 10.8 KB | Display Display | EMDB header |
Images | 1064.gif | 17.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1064 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1064 | HTTPS FTP |
-Validation report
Summary document | emd_1064_validation.pdf.gz | 222.8 KB | Display | EMDB validaton report |
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Full document | emd_1064_full_validation.pdf.gz | 221.9 KB | Display | |
Data in XML | emd_1064_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1064 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1064 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1064.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of the E.coli 70S/RF3 complex, state 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.419 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : 70S - RF3 complex E.coli
Entire | Name: 70S - RF3 complex E.coli |
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Components |
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-Supramolecule #1000: 70S - RF3 complex E.coli
Supramolecule | Name: 70S - RF3 complex E.coli / type: sample / ID: 1000 Details: two functional states within a single sample of homogeneous composition, separated by image processing techniques, state 1 Oligomeric state: monomer / Number unique components: 4 |
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Molecular weight | Theoretical: 2.5 MDa |
-Supramolecule #1: 70S
Supramolecule | Name: 70S / type: complex / ID: 1 / Name.synonym: 70S / Ribosome-details: ribosome-prokaryote: ALL |
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-Macromolecule #1: messenger RNA
Macromolecule | Name: messenger RNA / type: rna / ID: 1 / Name.synonym: mRNA / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / synonym: Escherichia coli |
Sequence | String: GGGCCCUUGU UAACAAUUAA GGAGGUAUAC UAUGUUUACG AUUUAAUUGC AGAAAAAAAA AAAAAAAAAA AAA |
-Macromolecule #2: isoleucin transfer RNA
Macromolecule | Name: isoleucin transfer RNA / type: rna / ID: 2 / Name.synonym: Ile-tRNA / Classification: TRANSFER / Structure: SINGLE STRANDED / Synthetic?: No |
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Source (natural) | Organism: Escherichia coli (E. coli) / synonym: Escherichia coli |
-Macromolecule #3: release factor 3
Macromolecule | Name: release factor 3 / type: protein_or_peptide / ID: 3 / Name.synonym: RF3 / Details: PrfC gene / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / synonym: Escherichia coli / Cell: Escherichia coli |
Recombinant expression | Organism: Escherichia coli MKH13 / Recombinant plasmid: pOSEX3 |
Sequence | InterPro: Peptide chain release factor 3 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.15 mg/mL |
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Buffer | pH: 7.5 / Details: polymix buffer |
Staining | Type: NEGATIVE / Details: no staining, cryo-EM with holey carbon grids |
Grid | Details: 300 mesh Cu/Rh |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: home-made cryo-plunger / Method: Blot for 2 seconds before plunging |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Alignment procedure | Legacy - Astigmatism: lens astigmatism was corrected at 60,000 times magnification |
Date | Dec 19, 2001 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 3 µm / Number real images: 44 / Average electron dose: 10 e/Å2 / Details: IMAGE SCIENCE PATCHWORK DENSITOMETER / Bits/pixel: 12 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 48000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.1 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: individual particles |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: IMAGIC / Details: exact filtered back-projection / Number images used: 11071 |
Final angle assignment | Details: beta gamma |
Final two d classification | Number classes: 322 |