+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2373 | |||||||||
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Title | ribosome-RelA complex | |||||||||
Map data | reconstruction of ribosome-RelA complex | |||||||||
Sample |
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Keywords | ribosome / RelA / stringent response | |||||||||
Biological species | Thermus thermophilus (bacteria) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 14.5 Å | |||||||||
Authors | Agirrezabala X / Fernandez I / Kelley A / Gil-Carton D / Ramakrishnan V / Valle M | |||||||||
Citation | Journal: EMBO Rep / Year: 2013 Title: The ribosome triggers the stringent response by RelA via a highly distorted tRNA. Authors: Xabier Agirrezabala / Israel S Fernández / Ann C Kelley / David Gil Cartón / Venki Ramakrishnan / Mikel Valle / Abstract: The bacterial stringent response links nutrient starvation with the transcriptional control of genes. This process is initiated by the stringent factor RelA, which senses the presence of deacylated ...The bacterial stringent response links nutrient starvation with the transcriptional control of genes. This process is initiated by the stringent factor RelA, which senses the presence of deacylated tRNA in the ribosome as a symptom of amino-acid starvation to synthesize the alarmone (p)ppGpp. Here we report a cryo-EM study of RelA bound to ribosomes bearing cognate, deacylated tRNA in the A-site. The data show that RelA on the ribosome stabilizes an unusual distorted form of the tRNA, with the acceptor arm making contact with RelA and far from its normal location in the peptidyl transferase centre. | |||||||||
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_2373.map.gz | 33 MB | EMDB map data format | |
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Header (meta data) | emd-2373-v30.xml emd-2373.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
Images | EMD-2373-4.tif | 455.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2373 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2373 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2373.map.gz / Format: CCP4 / Size: 34.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | reconstruction of ribosome-RelA complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.75 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-RelA complex
Entire | Name: 70S-RelA complex |
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Components |
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-Supramolecule #1000: 70S-RelA complex
Supramolecule | Name: 70S-RelA complex / type: sample / ID: 1000 / Number unique components: 5 |
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Molecular weight | Theoretical: 2.5 MDa |
-Supramolecule #1: 70S ribosome
Supramolecule | Name: 70S ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: Thermus thermophilus (bacteria) |
Molecular weight | Theoretical: 2.5 MDa |
-Macromolecule #1: deacylated tRNA
Macromolecule | Name: deacylated tRNA / type: rna / ID: 1 / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No |
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Source (natural) | Organism: Thermus thermophilus (bacteria) |
-Macromolecule #2: tRNA
Macromolecule | Name: tRNA / type: rna / ID: 2 / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No |
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Source (natural) | Organism: Thermus thermophilus (bacteria) |
-Macromolecule #3: tRNA
Macromolecule | Name: tRNA / type: rna / ID: 3 / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No |
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Source (natural) | Organism: Thermus thermophilus (bacteria) |
-Macromolecule #4: RelA
Macromolecule | Name: RelA / type: protein_or_peptide / ID: 4 / Recombinant expression: No |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.25 mg/mL |
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Buffer | pH: 7.45 Details: 5mM Hepes-KOH pH 7.45, 50mM KCl, 10mM NH4Cl, 10mM Mg-acetate, 5mM beta-mercapto-ethanol |
Staining | Type: NEGATIVE / Details: cryo |
Grid | Details: Quantifoil grids (2/4) with thin carbon on top |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK I / Method: Blot for 3 seconds before plunging |
-Electron microscopy
Microscope | JEOL 2200FS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 40000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 40000 |
Specialist optics | Energy filter - Name: in-column Omega filter / Energy filter - Lower energy threshold: 15.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Alignment procedure | Legacy - Astigmatism: corrected at 100k |
Date | Jan 15, 2012 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 7 µm / Number real images: 425 / Average electron dose: 10 e/Å2 / Bits/pixel: 8 |
-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: 14.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: XMIPP, SPIDER / Number images used: 28791 |
Details | particles were selected by combining automated particle picking , multivariate data analysis and visual inspection |
-Atomic model buiding 1
Initial model | PDB ID: 2wrn |
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Software | Name: MDFF |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
-Atomic model buiding 2
Initial model | PDB ID: 2wro |
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Software | Name: MDFF |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |