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Yorodumi- EMDB-1003: Solution structure of the E. coli 70S ribosome at 11.5 A resolution. -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1003 | |||||||||
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Title | Solution structure of the E. coli 70S ribosome at 11.5 A resolution. | |||||||||
Map data | E. coli 70S Ribosome | |||||||||
Sample |
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Function / homology | Function and homology information regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding ...regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.5 Å | |||||||||
Authors | Gabashvili IS | |||||||||
Citation | Journal: Cell / Year: 2000 Title: Solution structure of the E. coli 70S ribosome at 11.5 A resolution. Authors: I S Gabashvili / R K Agrawal / C M Spahn / R A Grassucci / D I Svergun / J Frank / P Penczek / Abstract: Over 73,000 projections of the E. coli ribosome bound with formyl-methionyl initiator tRNAf(Met) were used to obtain an 11.5 A cryo-electron microscopy map of the complex. This map allows ...Over 73,000 projections of the E. coli ribosome bound with formyl-methionyl initiator tRNAf(Met) were used to obtain an 11.5 A cryo-electron microscopy map of the complex. This map allows identification of RNA helices, peripheral proteins, and intersubunit bridges. Comparison of double-stranded RNA regions and positions of proteins identified in both cryo-EM and X-ray maps indicates good overall agreement but points to rearrangements of ribosomal components required for the subunit association. Fitting of known components of the 50S stalk base region into the map defines the architecture of the GTPase-associated center and reveals a major change in the orientation of the alpha-sarcin-ricin loop. Analysis of the bridging connections between the subunits provides insight into the dynamic signaling mechanism between the ribosomal subunits. | |||||||||
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_1003.map.gz | 6.7 MB | EMDB map data format | |
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Header (meta data) | emd-1003-v30.xml emd-1003.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
Images | 1003.gif | 81.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1003 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1003 | HTTPS FTP |
-Validation report
Summary document | emd_1003_validation.pdf.gz | 336.9 KB | Display | EMDB validaton report |
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Full document | emd_1003_full_validation.pdf.gz | 336.4 KB | Display | |
Data in XML | emd_1003_validation.xml.gz | 5.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1003 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1003 | HTTPS FTP |
-Related structure data
Related structure data | 1eg0MC 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_1003.map.gz / Format: CCP4 / Size: 7.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | E. coli 70S Ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.93 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 : FMet-tRNAMet 70S Ribosome from E.coli
Entire | Name: FMet-tRNAMet 70S Ribosome from E.coli |
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Components |
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-Supramolecule #1000: FMet-tRNAMet 70S Ribosome from E.coli
Supramolecule | Name: FMet-tRNAMet 70S Ribosome from E.coli / type: sample / ID: 1000 Details: preparation and buffer conditions are as described in Malhotra et al., J. Mol. Biol. (1998) 280, 103-116 Number unique components: 3 |
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Molecular weight | Theoretical: 2.5 MDa |
-Supramolecule #1: 70S ribosome Escherichia coli
Supramolecule | Name: 70S ribosome Escherichia coli / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: LSU 50S |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: fMet-tRNA
Macromolecule | Name: fMet-tRNA / type: rna / ID: 1 / Classification: OTHER / Structure: DOUBLE HELIX / Synthetic?: No |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #2: MF-mRNA
Macromolecule | Name: MF-mRNA / type: rna / ID: 2 / Details: 46 nucleotides / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-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: 7.6 Details: 20 mM Hepes, 6 mM Mg(CH3COO)2 150 mM NH4Cl, 4 mM beta-Mercaptoethanol, 0.5 mM Spermine, 2 mM Spermidine. |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: 2 side blotting plunger / Method: Blot and plunge |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG/ST |
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Temperature | Average: 93 K |
Details | 25 % of data from Philips EM420 with LaB6 at 100kV |
Date | Oct 4, 1997 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PERKIN ELMER / Digitization - Sampling interval: 15 µm / Number real images: 239 / Average electron dose: 10 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: 51200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.34 µm / Nominal defocus min: 2.17 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Cryo Transfer / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: Wiener filtration of defocus group volumes |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER/WEB / Number images used: 73523 |
-Atomic model buiding 1
Software | Name: O |
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Details | manual fitting using O Mol_Id: 1; Molecule: S4 Ribosomal Protein; Chain: A; Other_Details: Modeled By Analogous Protein Of B. Stearothermophilus Taken From Pdb Entry 1C06 Mol_Id: 2; Molecule: S5 Ribosomal Protein; Chain: B; Other_Details: Modeled By Analogous Protein Of B. Stearothermophilus Taken From Pdb Entry 1Pkp Mol_Id: 3; Molecule: S6 Ribosomal Protein; Chain: C; Other_Details: Modeled By Analogous Protein Of T. Thermophilus Taken From Pdb Entry 1Ris Mol_Id: 4; Molecule: S7 Ribosomal Protein; Chain: D; Other_Details: Modeled By Analogous Protein Of T. Thermophilus Taken From Pdb Entry 1Rss Mol_Id: 5; Molecule: S8 Ribosomal Protein; Chain: E; Other_Details: Modeled By Analogous Protein Of T. Thermophilus Taken From Pdb Entry 1An7 Mol_Id: 6; Molecule: S15 Ribosomal Protein; Chain: F; Other_Details: Modeled By Analogous Protein Of B. Stearothermophilus Taken From Pdb Entry 1A32 Mol_Id: 7; Molecule: S17 Ribosomal Protein; Chain: G; Other_Details: Modeled By Analogous Protein Of B. Stearothermophilus Taken From Pdb Entries 1Rip and 1Qd7 Mol_Id: 8; Molecule: S20 Ribosomal Protein; Chain: H; Other_Details: Modeled By Analogous Protein Of T. Thermophilus Taken From Pdb Entry 1Qd7 Mol_Id: 9; Molecule: Ribosomal Protein L1; Chain: N; Other_Details: Modeled By Analogous Protein Of T. Thermophilus Taken From Pdb Entry 1Ad2 Mol_Id: 10; Molecule: Ribosomal Protein L6; Chain: J; Mutation: Yes; Other_Details: Modeled By Analogous Protein Of T. Stearothermophilus Taken From Pdb Entry 1Rl6 Mol_Id: 11; Molecule: Ribosomal Protein L11; Chain: K; Other_Details: Modeled By Analogous Protein Of T. Maritima Taken From Pdb Entry 1Mms Mol_Id: 12; Molecule: Fragment Of 16S Rrna Helix 23; Chain: I; Fragment: Residues 673-713; Other_Details: Modeled As Analogous Fragment Of T. Thermophilus Taken From Pdb Entry 1Qd7 Mol_Id: 13; Molecule: Fragment Of 23S Rrna; Chain: L; Fragment: Residues 1051-1108; Other_Details: T. Maritima RNA Sequence and Model Taken From Pdb Entry 1Mms Mol_Id: 14; Molecule: Helix 95 Of 23S Rrna; Chain: M; Other_Details: E. Coli RNA Sequence and Model Taken From Pdb Entry 480D Mol_Id: 15; Molecule: Formyl-Methionyl-tRNA; Chain: O; Synonym: Fmet-tRNA; Other_Details: E. Coli Fmet-tRNA Sequence and Model Taken From Pdb Entry 2Fmt |
Refinement | Protocol: RIGID BODY FIT |
Output model | PDB-1eg0: |