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- EMDB-5364: New mRNA-tRNA translocation intermediates revealed by cryoEM: Cla... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5364 | |||||||||
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Title | New mRNA-tRNA translocation intermediates revealed by cryoEM: Class 4B (partially rotated (II) 70S ribosome with A-site and P-site tRNAs) | |||||||||
![]() | Cry-EM revealed partially rotated (ii) 70S ribosome with A and P site tRNAs (Class 4B) | |||||||||
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![]() | ribosome / 70S / partially rotated / intermediates / translocation / tRNA | |||||||||
Function / homology | ![]() 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 / translational termination / DnaA-L2 complex / four-way junction DNA binding / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication 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 / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / transcription antitermination / response to reactive oxygen species / translational initiation / regulation of cell growth / ribosomal large subunit assembly / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / rRNA binding / negative regulation of translation / 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 | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.5 Å | |||||||||
![]() | Agirrezabala X / Liao HY / Schreiner E / Fu J / Ortiz-Meoz RF / Schulten K / Green R / Frank J | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 54.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.6 KB 11.6 KB | Display Display | ![]() |
Images | ![]() | 82.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4v6pMC ![]() 5359C ![]() 5360C ![]() 5361C ![]() 5362C ![]() 5363C ![]() 4v6nC ![]() 4v6oC ![]() 4v6qC ![]() 4v6rC ![]() 4v6sC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cry-EM revealed partially rotated (ii) 70S ribosome with A and P site tRNAs (Class 4B) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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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: 3 |
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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: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 6 seconds |
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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: ![]() |
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 |
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Image processing
CTF correction | Details: defocus groups, Wiener filter |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 13.5 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-4v6p: |
-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-4v6p: |