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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
TitleCoordinates of 16S and 23S rRNAs fitted into the cryo-EM map of a pretranslocation complex
Components
  • 16S Ribosomal RNA from E. coli
  • 23S Ribosomal RNA from E. coli
KeywordsRIBOSOME / pretranslocation / ratchet motion
Function / homologyRNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10 Å
AuthorsGao, H. / LeBarron, J. / Frank, J.
CitationJournal: To be published
Title: Ribosomal Dynamics: Intrinsic Instability of a Moleculaar Machine
Authors: Gao, H. / LeBarron, J. / Frank, J.
History
DepositionJun 12, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 2019Group: Data collection / Database references / Other
Category: cell / citation ...cell / citation / database_2 / em_image_scans
Item: _cell.length_a / _cell.length_b ..._cell.length_a / _cell.length_b / _cell.length_c / _citation.year
Revision 1.3Dec 18, 2019Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-1056
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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
Polymers1,441,3022
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 499690.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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 method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
Sequence detailsTHE STRUCTURE CONTAINS P ATOMS ONLY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: E. coli 70S ribosome bound with 3 tRNAs / Type: RIBOSOME
Buffer solutionName: polymix / pH: 7.5 / Details: polymix
SpecimenConc.: 32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Details: Rapid freezing in liquid ethane

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 49696 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1RSRefmodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: CTF correction of 3D map
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: 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 buildingProtocol: 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
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
12AVY

2avy
PDB Unreleased entry

12AVY1PDBexperimental model
22AW4

2aw4
PDB Unreleased entry

12AW42PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4371 0 0 4371

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