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- PDB-3dg2: Coordinates of 16S and 23S rRNAs fitted into the cryo-EM map of a... -
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Basic information
Entry | Database: PDB / ID: 3dg2 | ||||||
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Title | Coordinates of 16S and 23S rRNAs fitted into the cryo-EM map of a pretranslocation complex | ||||||
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![]() | RIBOSOME / pretranslocation / ratchet motion | ||||||
Function / homology | RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10 Å | ||||||
![]() | Gao, H. / LeBarron, J. / Frank, J. | ||||||
![]() | ![]() Title: Ribosomal Dynamics: Intrinsic Instability of a Moleculaar Machine Authors: Gao, H. / LeBarron, J. / Frank, J. | ||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.3 KB | Display | ![]() |
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PDB format | ![]() | 82 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1056M ![]() 3dg0C ![]() 3dg4C ![]() 3dg5C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: RNA chain | Mass: 499690.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: RNA chain | Mass: 941612.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
Sequence details | THE STRUCTURE CONTAINS P ATOMS ONLY |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: E. coli 70S ribosome bound with 3 tRNAs / Type: RIBOSOME |
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Buffer solution | Name: polymix / pH: 7.5 / Details: polymix |
Specimen | Conc.: 32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Details: Rapid freezing in liquid ethane |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 49696 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm |
Specimen holder | Temperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
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Processing
EM software |
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CTF correction | Details: CTF correction of 3D map | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Method: reference-based alignment / Resolution: 10 Å / Num. of particles: 52181 / Nominal pixel size: 2.8 Å / Actual pixel size: 2.76 Å / Magnification calibration: TMV / Details: SPIDER package / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Target criteria: cross-correlation coefficient, real-space R factor Details: METHOD--Auto REFINEMENT PROTOCOL--multi-rigid body, real-space refinement | |||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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