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- PDB-3dg4: Coordinates of 16S and 23S rRNAs fitted into the cryo-EM map of R... -

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Database: PDB / ID: 3dg4
TitleCoordinates of 16S and 23S rRNAs fitted into the cryo-EM map of RF1-bound termination complex
  • 16S Ribosomal RNA from E. coli
  • 23S RibosomaL RNA from E. coli
KeywordsRIBOSOME / Ribosome / termination / ratchet motion
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 12.8 Å resolution
AuthorsGao, H. / LeBarron, J. / Frank, J.
CitationJournal: To be published / Year: 2009
Title: Ribosomal Dynamics: Intrinsic Instability of a Moleculaar Machine
Authors: Gao, H. / LeBarron, J. / Frank, J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 12, 2008 / Release: Feb 3, 2009
RevisionDateData content typeGroupProviderType
1.0Feb 3, 2009Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

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Deposited unit
A: 16S Ribosomal RNA from E. coli
B: 23S RibosomaL RNA from E. coli

Theoretical massNumber of molelcules
Total (without water)1,441,3022

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1


#1: RNA chain 16S Ribosomal RNA from E. coli / / Coordinate model: P atoms only

Mass: 499690.031 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli)
#2: RNA chain 23S RibosomaL RNA from E. coli / / Coordinate model: P atoms only

Mass: 941612.375 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli)

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

Sample preparation

ComponentName: E. coli 70S ribosome bound with RF1 / Type: RIBOSOME
Buffer solutionName: polymix / Details: polymix / pH: 7.5
SpecimenConc.: 32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: Rapid freezing in liquid ethane

Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20 / Date: Dec 1, 2002
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 / Calibrated magnification: 49696 / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Specimen holderTemperature: 93 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM


EM software
1RSRefmodel fittingTNT
2SPIDER3D reconstruction
CTF correctionDetails: CTF correction of 3D map
SymmetryPoint symmetry: C1
3D reconstructionMethod: reference-based alignment / Resolution: 12.8 Å / Number of particles: 24622 / Nominal pixel size: 2.8 / Actual pixel size: 2.76 / Magnification calibration: TMV / Details: SPIDER package / Symmetry type: POINT
Atomic model buildingDetails: METHOD--Auto REFINEMENT PROTOCOL--multi-rigid body, real-space refinement
Ref protocol: RIGID BODY FIT / Ref space: REAL
Target criteria: cross-correlation coefficient, real-space R factor
Atomic model building
IDPDB-ID 3D fitting ID
Number of atoms included #LASTProtein: 0 / Nucleic acid: 4371 / Ligand: 0 / Solvent: 0 / Total: 4371

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