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Yorodumi- EMDB-1007: A cryo-electron microscopic study of ribosome-bound termination f... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1007 | |||||||||
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Title | A cryo-electron microscopic study of ribosome-bound termination factor RF2. | |||||||||
Map data | Ribosome-bound termination factor RF2 | |||||||||
Sample |
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Function / homology | Function and homology information translation release factor activity, codon specific / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / translational termination / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / structural constituent of ribosome / translation / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.9 Å | |||||||||
Authors | Rawat UB / Zavialov AV / Sengupta J / Valle M / Grassucci RA / Linde J / Vestergaard B / Ehrenberg M / Frank J | |||||||||
Citation | Journal: Nature / Year: 2003 Title: A cryo-electron microscopic study of ribosome-bound termination factor RF2. Authors: Urmila B S Rawat / Andrey V Zavialov / Jayati Sengupta / Mikel Valle / Robert A Grassucci / Jamie Linde / Bente Vestergaard / Måns Ehrenberg / Joachim Frank / Abstract: Protein synthesis takes place on the ribosome, where genetic information carried by messenger RNA is translated into a sequence of amino acids. This process is terminated when a stop codon moves into ...Protein synthesis takes place on the ribosome, where genetic information carried by messenger RNA is translated into a sequence of amino acids. This process is terminated when a stop codon moves into the ribosomal decoding centre (DC) and is recognized by a class-1 release factor (RF). RFs have a conserved GGQ amino-acid motif, which is crucial for peptide release and is believed to interact directly with the peptidyl-transferase centre (PTC) of the 50S ribosomal subunit. Another conserved motif of RFs (SPF in RF2) has been proposed to interact directly with stop codons in the DC of the 30S subunit. The distance between the DC and PTC is approximately 73 A. However, in the X-ray structure of RF2, SPF and GGQ are only 23 A apart, indicating that they cannot be at DC and PTC simultaneously. Here we show that RF2 is in an open conformation when bound to the ribosome, allowing GGQ to reach the PTC while still allowing SPF-stop-codon interaction. The results indicate new interpretations of accuracy in termination, and have implications for how the presence of a stop codon in the DC is signalled to PTC. | |||||||||
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_1007.map.gz | 7.9 MB | EMDB map data format | |
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Header (meta data) | emd-1007-v30.xml emd-1007.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
Images | 1007.gif | 26.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1007 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1007 | HTTPS FTP |
-Validation report
Summary document | emd_1007_validation.pdf.gz | 337.1 KB | Display | EMDB validaton report |
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Full document | emd_1007_full_validation.pdf.gz | 336.7 KB | Display | |
Data in XML | emd_1007_validation.xml.gz | 5.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1007 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1007 | HTTPS FTP |
-Related structure data
Related structure data | 1mi6MC 1mvrMC 1006C 1008C 1009C 1010C 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_1007.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Ribosome-bound termination factor RF2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 ribosome-RF2(wild type) complex
Entire | Name: E.coli 70s ribosome-RF2(wild type) complex |
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Components |
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-Supramolecule #1000: E.coli 70s ribosome-RF2(wild type) complex
Supramolecule | Name: E.coli 70s ribosome-RF2(wild type) complex / type: sample / ID: 1000 / Number unique components: 5 |
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Molecular weight | Theoretical: 2.5 MDa |
-Supramolecule #1: E.coli 70S ribosome
Supramolecule | Name: E.coli 70S ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: LSU 50S |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 2.5 MDa |
-Macromolecule #1: P-tRNA
Macromolecule | Name: P-tRNA / type: ligand / ID: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #2: E-tRNA
Macromolecule | Name: E-tRNA / type: ligand / ID: 2 / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #3: MFTI-mRNA
Macromolecule | Name: MFTI-mRNA / type: ligand / ID: 3 Details: Zavialov et al., A posttermination ribosomal complex is the guanine nucleotide exchange factor for peptide release factor RF3. Cell. 107,1-20 (2001). Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #4: RF2 (GGQ) wild type
Macromolecule | Name: RF2 (GGQ) wild type / type: ligand / ID: 4 / Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / Location in cell: cytoplasm |
Recombinant expression | Organism: Escherichia coli BL12 (DE3) / Recombinant plasmid: pET11a |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.09 mg/mL |
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Buffer | pH: 7.5 Details: Polymix buffer,containing at final concentration 5mM potassium phosphate, 5mM magnesium acetate, 5mM ammonium chloride, 95 mM potassium chloride, 0.5 mM calcium chloride, 8mM putrescine, 1mM ...Details: Polymix buffer,containing at final concentration 5mM potassium phosphate, 5mM magnesium acetate, 5mM ammonium chloride, 95 mM potassium chloride, 0.5 mM calcium chloride, 8mM putrescine, 1mM spermidine and 1mM dithioerythritol |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 58 % / Chamber temperature: 36 K / Instrument: HOMEMADE PLUNGER Details: Vitrification instrument: Two side blotting plunger Method: Blot and Plunge |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 93 K |
Date | Oct 8, 2001 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 41 / Average electron dose: 20 e/Å2 / Bits/pixel: 12 |
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: 4.5 µm / Nominal defocus min: 2.02 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Oxford, Cryo-transfer 3500 / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Wiener filtration of defocus groups |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER/WEB Details: Frank, J. (2000) Three-Dimensional Cryoelectron Microscopy of Ribosomes, Methods of Enzymology (Ch.18) 317, 276-291. Number images used: 18199 |
-Atomic model buiding 1
Initial model | (PDB ID: , ) |
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Software | Name: O |
Details | manual fitting using O |
Refinement | Protocol: RIGID BODY FIT |
Output model | PDB-1mi6: PDB-1mvr: |