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- PDB-1zo3: The P-site and P/E-site tRNA structures fitted to P/I site codon. -

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Basic information

Entry
Database: PDB / ID: 1zo3
TitleThe P-site and P/E-site tRNA structures fitted to P/I site codon.
ComponentstRNATransfer RNA
KeywordsRNA / E. COLI / RIBOSOME / INITIATION OF PROTEIN SYNTHESIS / INITIATION FACTOR / CRYO-ELETRON MICROSCOPY
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13.8 Å
AuthorsAllen, G.S. / Zavialov, A. / Gursky, R. / Ehrenberg, M. / Frank, J.
CitationJournal: Cell / Year: 2005
Title: The cryo-EM structure of a translation initiation complex from Escherichia coli.
Authors: Gregory S Allen / Andrey Zavialov / Richard Gursky / Måns Ehrenberg / Joachim Frank /
Abstract: The 70S ribosome and its complement of factors required for initiation of translation in E. coli were purified separately and reassembled in vitro with GDPNP, producing a stable initiation complex ...The 70S ribosome and its complement of factors required for initiation of translation in E. coli were purified separately and reassembled in vitro with GDPNP, producing a stable initiation complex (IC) stalled after 70S assembly. We have obtained a cryo-EM reconstruction of the IC showing IF2*GDPNP at the intersubunit cleft of the 70S ribosome. IF2*GDPNP contacts the 30S and 50S subunits as well as fMet-tRNA(fMet). IF2 here adopts a conformation radically different from that seen in the recent crystal structure of IF2. The C-terminal domain of IF2 binds to the single-stranded portion of fMet-tRNA(fMet), thereby forcing the tRNA into a novel orientation at the P site. The GTP binding domain of IF2 binds to the GTPase-associated center of the 50S subunit in a manner similar to EF-G and EF-Tu. Additionally, we present evidence for the localization of IF1, IF3, one C-terminal domain of L7/L12, and the N-terminal domain of IF2 in the initiation complex.
History
DepositionMay 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell / em_image_scans
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: tRNA
B: tRNA


Theoretical massNumber of molelcules
Total (without water)49,0372
Polymers49,0372
Non-polymers00
Water0
1


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

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Components

#1: RNA chain tRNA / Transfer RNA


Mass: 24518.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: P-site and P/E-site tRNA / Source: (natural) Escherichia coli (E. coli)

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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: 70S INITIATION COMPLEX / Type: RIBOSOME
Buffer solutionName: POLYMIX BUFFER / pH: 7.5 / Details: POLYMIX BUFFER
SpecimenConc.: 0.032 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE
Details: HOLEY CARBON GRID AT 20C, FLASH FROZEN INTO LIQUID ETHAN

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jan 1, 2004 / Details: LOW DOSE MODE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 X / Nominal defocus max: -3930 nm / Nominal defocus min: -930 nm / Cs: 2 mm
Specimen holderTemperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingFilm or detector model: KODAK SO-163 FILM

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Processing

CTF correctionDetails: DEFOCUS GROUPS 0.93-3.93 UM
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: MULTI-REFERENCE / Resolution: 13.8 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 20283 / Nominal pixel size: 2.82 Å / Actual pixel size: 2.82 Å
Details: resolution 13.8 ANGSTROMS (FSC=0.5) and 8.6 ANGSTROMS (3sigma)
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: BEST FIT USING RSREF
Details: REFINEMENT PROTOCOL--RIGID BODY FIT OF TRNA DETAILS--the tRNA coordinate files were fitted to the E. coli translation initiation complex map (EMBL-EMD 3525) in the following way- first the ...Details: REFINEMENT PROTOCOL--RIGID BODY FIT OF TRNA DETAILS--the tRNA coordinate files were fitted to the E. coli translation initiation complex map (EMBL-EMD 3525) in the following way- first the cross-correlation of the respective 30S subunit maps were maximized and the resulting transformation matrix was computed. second the coordinates of the tRNA models were transformed according to the matrix previously computed.
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3250 0 0 3250

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