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Yorodumi- PDB-3dg5: Coordinates of 16S and 23S rRNAs fitted into the cryo-EM map of R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dg5 | ||||||
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Title | Coordinates of 16S and 23S rRNAs fitted into the cryo-EM map of RF3-bound termination complex | ||||||
Components |
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Keywords | RIBOSOME / termination / ratchet motion | ||||||
Function / homology | RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 15.5 Å | ||||||
Authors | Gao, H. / LeBarron, J. / Frank, J. | ||||||
Citation | Journal: To be published Title: Ribosomal Dynamics: Intrinsic Instability of a Moleculaar Machine Authors: Gao, H. / LeBarron, J. / Frank, J. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3dg5.cif.gz | 140.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dg5.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 3dg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dg5_validation.pdf.gz | 799.8 KB | Display | wwPDB validaton report |
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Full document | 3dg5_full_validation.pdf.gz | 799.4 KB | Display | |
Data in XML | 3dg5_validation.xml.gz | 45.9 KB | Display | |
Data in CIF | 3dg5_validation.cif.gz | 74 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/3dg5 ftp://data.pdbj.org/pub/pdb/validation_reports/dg/3dg5 | HTTPS FTP |
-Related structure data
Related structure data | 1302M 3dg0C 3dg2C 3dg4C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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) Escherichia coli (E. coli) |
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#2: RNA chain | Mass: 941612.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
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 |
-Sample preparation
Component | Name: E. coli 70S ribosome bound with RF3-GDPNP / 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 | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: Rapid freezing in liquid ethane |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Jan 30, 2002 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
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 |
-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: 15.5 Å / Num. of particles: 45000 / 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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