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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1363 | |||||||||
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Title | Locking and unlocking of ribosomal motions. | |||||||||
![]() | Cryo-EM map of E.coli 70S ribosome | |||||||||
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Function / homology | ![]() ribosome disassembly / translational elongation / translation elongation factor activity / GDP binding / ribosome binding / small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding ...ribosome disassembly / translational elongation / translation elongation factor activity / GDP binding / ribosome binding / small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / GTPase activity / GTP binding / magnesium ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.9 Å | |||||||||
![]() | Mikel V / Andrey Z / Sengupta J / Rawat U / Ehrenberg M / Frank J | |||||||||
![]() | ![]() Title: Locking and unlocking of ribosomal motions. Authors: Mikel Valle / Andrey Zavialov / Jayati Sengupta / Urmila Rawat / Måns Ehrenberg / Joachim Frank / ![]() Abstract: During the ribosomal translocation, the binding of elongation factor G (EF-G) to the pretranslocational ribosome leads to a ratchet-like rotation of the 30S subunit relative to the 50S subunit in the ...During the ribosomal translocation, the binding of elongation factor G (EF-G) to the pretranslocational ribosome leads to a ratchet-like rotation of the 30S subunit relative to the 50S subunit in the direction of the mRNA movement. By means of cryo-electron microscopy we observe that this rotation is accompanied by a 20 A movement of the L1 stalk of the 50S subunit, implying that this region is involved in the translocation of deacylated tRNAs from the P to the E site. These ribosomal motions can occur only when the P-site tRNA is deacylated. Prior to peptidyl-transfer to the A-site tRNA or peptide removal, the presence of the charged P-site tRNA locks the ribosome and prohibits both of these motions. | |||||||||
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 | ![]() | 7.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.5 KB 9.5 KB | Display Display | ![]() |
Images | ![]() | 60.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 342.7 KB | Display | ![]() |
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Full document | ![]() | 342.3 KB | Display | |
Data in XML | ![]() | 5.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pn6MC ![]() 1pn7MC ![]() 1pn8MC ![]() 2z9qM ![]() 3dg0M ![]() 3iyyM ![]() 1362C ![]() 1364C ![]() 1365C ![]() 1366C ![]() 3izpF |
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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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of E.coli 70S ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Sample components
-Entire : EF-G bound Release Complex in the presence of Puromycin and GDPNP
Entire | Name: EF-G bound Release Complex in the presence of Puromycin and GDPNP |
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Components |
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-Supramolecule #1000: EF-G bound Release Complex in the presence of Puromycin and GDPNP
Supramolecule | Name: EF-G bound Release Complex in the presence of Puromycin and GDPNP type: sample / ID: 1000 / Number unique components: 4 |
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-Supramolecule #1: Release Complex
Supramolecule | Name: Release Complex / type: complex / ID: 1 / Details: mRNA and tRNA / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Puromycin
Macromolecule | Name: Puromycin / type: ligand / ID: 1 / Details: Antibiotic / Recombinant expression: No |
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Source (natural) | Organism: synthetic construct (others) |
Chemical component information | ![]() ChemComp-PUY: |
-Macromolecule #2: EF-G
Macromolecule | Name: EF-G / type: ligand / ID: 2 / Recombinant expression: No |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #3: GDPNP
Macromolecule | Name: GDPNP / type: ligand / ID: 3 / Recombinant expression: No |
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Source (natural) | Organism: synthetic construct (others) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: OTHER / Details: Rapid-freezing in liquid ethane |
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Electron microscopy
Microscope | FEI TECNAI 20 |
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Temperature | Average: 93 K |
Alignment procedure | Legacy - Electron beam tilt params: 0 |
Date | Jul 11, 2003 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 49696 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000 |
Sample stage | Specimen holder: cryo transfer / Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
CTF correction | Details: CTF correctionn of 3D map |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, package / Number images used: 1 |