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Yorodumi- EMDB-1302: RF3 induces ribosomal conformational changes responsible for diss... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1302 | |||||||||
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Title | RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors. | |||||||||
Map data | This is the map of a ribosome. | |||||||||
Sample |
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Function / homology | Function and homology information regulation of translational termination / translation release factor activity, codon nonspecific / translation release factor activity, codon specific / guanosine tetraphosphate binding / translational termination / maintenance of translational fidelity / GDP binding / GTPase activity / GTP binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 15.5 Å | |||||||||
Authors | Gao H / Zhou Z / Rawat U / Huang C / Bouakaz L / Wang C / Liu Y / Zavialov A / Gursky R / Sanyal S ...Gao H / Zhou Z / Rawat U / Huang C / Bouakaz L / Wang C / Liu Y / Zavialov A / Gursky R / Sanyal S / Ehrenberg M / Frank J / Song H | |||||||||
Citation | Journal: Cell / Year: 2007 Title: RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors. Authors: Haixiao Gao / Zhihong Zhou / Urmila Rawat / Chenhui Huang / Lamine Bouakaz / Chernhoe Wang / Zhihong Cheng / Yuying Liu / Andrey Zavialov / Richard Gursky / Suparna Sanyal / Måns Ehrenberg ...Authors: Haixiao Gao / Zhihong Zhou / Urmila Rawat / Chenhui Huang / Lamine Bouakaz / Chernhoe Wang / Zhihong Cheng / Yuying Liu / Andrey Zavialov / Richard Gursky / Suparna Sanyal / Måns Ehrenberg / Joachim Frank / Haiwei Song / Abstract: During translation termination, class II release factor RF3 binds to the ribosome to promote rapid dissociation of a class I release factor (RF) in a GTP-dependent manner. We present the crystal ...During translation termination, class II release factor RF3 binds to the ribosome to promote rapid dissociation of a class I release factor (RF) in a GTP-dependent manner. We present the crystal structure of E. coli RF3*GDP, which has a three-domain architecture strikingly similar to the structure of EF-Tu*GTP. Biochemical data on RF3 mutants show that a surface region involving domains II and III is important for distinct steps in the action cycle of RF3. Furthermore, we present a cryo-electron microscopy (cryo-EM) structure of the posttermination ribosome bound with RF3 in the GTP form. Our data show that RF3*GTP binding induces large conformational changes in the ribosome, which break the interactions of the class I RF with both the decoding center and the GTPase-associated center of the ribosome, apparently leading to the release of the class I RF. | |||||||||
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_1302.map.gz | 7.6 MB | EMDB map data format | |
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Header (meta data) | emd-1302-v30.xml emd-1302.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | 1302.gif | 48.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1302 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1302 | HTTPS FTP |
-Validation report
Summary document | emd_1302_validation.pdf.gz | 315.5 KB | Display | EMDB validaton report |
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Full document | emd_1302_full_validation.pdf.gz | 315.1 KB | Display | |
Data in XML | emd_1302_validation.xml.gz | 5.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1302 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1302 | HTTPS FTP |
-Related structure data
Related structure data | 2o0fMC 3dg5M 2h5eC M: atomic model generated by this map C: citing same article (ref.) |
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Similar 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_1302.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is the map of a ribosome. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : E.coli 70s ribosomal release complex bound with RF3
Entire | Name: E.coli 70s ribosomal release complex bound with RF3 |
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Components |
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-Supramolecule #1000: E.coli 70s ribosomal release complex bound with RF3
Supramolecule | Name: E.coli 70s ribosomal release complex bound with RF3 / type: sample / ID: 1000 / Number unique components: 3 |
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-Supramolecule #1: 70s
Supramolecule | Name: 70s / type: complex / ID: 1 / Details: E.coli / Ribosome-details: ribosome-prokaryote: ALL |
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-Macromolecule #1: RF3
Macromolecule | Name: RF3 / type: protein_or_peptide / ID: 1 / Details: E.coli / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No |
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Source (natural) | Organism: Escherichia coli (E. coli) / synonym: E.coli |
-Macromolecule #2: tRNA
Macromolecule | Name: tRNA / type: rna / ID: 2 / Details: Hybrid P/E / Classification: OTHER / Structure: OTHER / Synthetic?: No |
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Source (natural) | Organism: Escherichia coli (E. coli) / synonym: E.coli |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: Polymix |
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Staining | Type: NEGATIVE / Details: Cryo |
Grid | Details: Quanti-foil grids coated with a thin carbon layer |
Vitrification | Cryogen name: ETHANE / Instrument: OTHER Details: Vitrification instrument: Vitrobot. Rapid-freezing in liquid ethane |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 93 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification Legacy - Electron beam tilt params: 0 |
Date | Jan 30, 2002 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Average electron dose: 20 e/Å2 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 49696 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: cryo transfer / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: CTF correctionn of 3D map |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER package / Number images used: 45000 |
-Atomic model buiding 1
Initial model | PDB ID: 2avy Chain - Chain ID: A |
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Software | Name: RSRef, TNT |
Details | Protocol: Rigid Body. Real-space refinement using RSRef. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross correlation coefficient |
Output model | PDB-2o0f: PDB-3dg5: |
-Atomic model buiding 2
Initial model | PDB ID: 2aw4 Chain - Chain ID: A |
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Software | Name: RSRef, TNT |
Details | Protocol: Rigid Body. Real-space refinement using RSRef. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross correlation coefficient |
Output model | PDB-2o0f: PDB-3dg5: |