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Yorodumi- EMDB-5360: New mRNA-tRNA translocation intermediates revealed by cryoEM: Cla... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5360 | |||||||||
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Title | New mRNA-tRNA translocation intermediates revealed by cryoEM: Class 3 (unrotated 70S ribosome with P-site tRNA) | |||||||||
Map data | Cryo revealed unrotated ribosome with P tRNA (Class 3). | |||||||||
Sample |
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Keywords | ribosome / 70S / unrotated / intermediates / translocation / tRNA | |||||||||
Function / homology | Function and homology information negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / four-way junction DNA binding / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / negative regulation of translational initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / DNA endonuclease activity / response to reactive oxygen species / transcription antitermination / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / large ribosomal subunit / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / molecular adaptor activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.1 Å | |||||||||
Authors | Agirrezabala X / Liao HY / Schreiner E / Fu J / Ortiz-Meoz RF / Schulten K / Green R / Frank J | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2012 Title: Structural characterization of mRNA-tRNA translocation intermediates. Authors: Xabier Agirrezabala / Hstau Y Liao / Eduard Schreiner / Jie Fu / Rodrigo F Ortiz-Meoz / Klaus Schulten / Rachel Green / Joachim Frank / Abstract: Cryo-EM analysis of a wild-type Escherichia coli pretranslocational sample has revealed the presence of previously unseen intermediate substates of the bacterial ribosome during the first phase of ...Cryo-EM analysis of a wild-type Escherichia coli pretranslocational sample has revealed the presence of previously unseen intermediate substates of the bacterial ribosome during the first phase of translocation, characterized by intermediate intersubunit rotations, L1 stalk positions, and tRNA configurations. Furthermore, we describe the domain rearrangements in quantitative terms, which has allowed us to characterize the processivity and coordination of the conformational reorganization of the ribosome, along with the associated changes in tRNA ribosome-binding configuration. The results are consistent with the view of the ribosome as a molecular machine employing Brownian motion to reach a functionally productive state via a series of substates with incremental changes in conformation. | |||||||||
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_5360.map.gz | 54.9 MB | EMDB map data format | |
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Header (meta data) | emd-5360-v30.xml emd-5360.xml | 11.5 KB 11.5 KB | Display Display | EMDB header |
Images | emd_5360_1.gif | 92.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5360 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5360 | HTTPS FTP |
-Validation report
Summary document | emd_5360_validation.pdf.gz | 329 KB | Display | EMDB validaton report |
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Full document | emd_5360_full_validation.pdf.gz | 328.6 KB | Display | |
Data in XML | emd_5360_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5360 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5360 | HTTPS FTP |
-Related structure data
Related structure data | 4v6sMC 5359C 5361C 5362C 5363C 5364C 4v6nC 4v6oC 4v6pC 4v6qC 4v6rC 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_5360.map.gz / Format: CCP4 / Size: 58.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo revealed unrotated ribosome with P tRNA (Class 3). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.5 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 : Trp-tRNA-EFTu-GDP-kir-70S ribosome
Entire | Name: Trp-tRNA-EFTu-GDP-kir-70S ribosome |
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Components |
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-Supramolecule #1000: Trp-tRNA-EFTu-GDP-kir-70S ribosome
Supramolecule | Name: Trp-tRNA-EFTu-GDP-kir-70S ribosome / type: sample / ID: 1000 / Oligomeric state: monomeric / Number unique components: 2 |
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Molecular weight | Experimental: 2.8 MDa / Theoretical: 2.8 MDa |
-Supramolecule #1: 70S ribosome
Supramolecule | Name: 70S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: ALL |
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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 | 0.03 mg/mL |
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Buffer | pH: 7.5 Details: HiFi buffer (50 mM Tris-HCl, pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2) |
Grid | Details: 200 mesh |
Vitrification | Cryogen name: NITROGEN / Chamber humidity: 90 % / Chamber temperature: 80 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: blot for 3 seconds |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Temperature | Min: 80.7 K / Max: 80.7 K / Average: 80.7 K |
Alignment procedure | Legacy - Astigmatism: objective corrected at 100,000 times magnification Legacy - Electron beam tilt params: no tilt |
Specialist optics | Energy filter - Name: no filter |
Details | automated data collection system AutoEMation (CCD mag. 100000x) |
Date | May 1, 2007 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 25 e/Å2 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 58269 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder: cartridge / Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: defocus groups, Wiener filter |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 13.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: XMIPP, SPIDER / Details: Classification using ML3D / Number images used: 21000 |
-Atomic model buiding 1
Initial model | PDB ID: 2i2u |
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Software | Name: MDFF |
Details | Protocol: Molecular Dynamics based flexible fitting |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: RMSD, cross correlation |
Output model | PDB-4v6s: |
-Atomic model buiding 2
Initial model | PDB ID: 2i2v |
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Software | Name: MDFF |
Details | Protocol: Molecular Dynamics based flexible fitting |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: RMSD, cross correlation |
Output model | PDB-4v6s: |