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- PDB-1fcw: TRNA POSITIONS DURING THE ELONGATION CYCLE -

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Basic information

Entry
Database: PDB / ID: 1fcw
TitleTRNA POSITIONS DURING THE ELONGATION CYCLE
ComponentsTRNAPHE
KeywordsRIBOSOME / tRNA binding sites / protein synthesis / elongation cycle
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 17 Å
AuthorsAgrawal, R.K. / Spahn, C.M.T. / Penczek, P. / Grassucci, R.A. / Nierhaus, K.H. / Frank, J.
CitationJournal: J Cell Biol / Year: 2000
Title: Visualization of tRNA movements on the Escherichia coli 70S ribosome during the elongation cycle.
Authors: R K Agrawal / C M Spahn / P Penczek / R A Grassucci / K H Nierhaus / J Frank /
Abstract: Three-dimensional cryomaps have been reconstructed for tRNA-ribosome complexes in pre- and posttranslocational states at 17-A resolution. The positions of tRNAs in the A and P sites in the ...Three-dimensional cryomaps have been reconstructed for tRNA-ribosome complexes in pre- and posttranslocational states at 17-A resolution. The positions of tRNAs in the A and P sites in the pretranslocational complexes and in the P and E sites in the posttranslocational complexes have been determined. Of these, the P-site tRNA position is the same as seen earlier in the initiation-like fMet-tRNA(f)(Met)-ribosome complex, where it was visualized with high accuracy. Now, the positions of the A- and E-site tRNAs are determined with similar accuracy. The positions of the CCA end of the tRNAs at the A site are different before and after peptide bond formation. The relative positions of anticodons of P- and E-site tRNAs in the posttranslocational state are such that a codon-anticodon interaction at the E site appears feasible.
History
DepositionJul 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

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Assembly

Deposited unit
A: TRNAPHE
B: TRNAPHE
C: TRNAPHE
D: TRNAPHE
E: TRNAPHE


Theoretical massNumber of molelcules
Total (without water)124,4515
Polymers124,4515
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
TRNAPHE


Mass: 24890.121 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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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: tRNA-Ribosome complex / Type: COMPLEX / Source: MULTIPLE SOURCES
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Crystal grow
*PLUS
Method: other / Details: electron microscopy

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS EM420
Electron gunElectron source: OTHER / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 52200 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Specimen holderSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingElectron dose: 10 e/Å2 / Film or detector model: GENERIC FILM
Image scansScanner model: PERKIN ELMER

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Processing

SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 17 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Num. of particles: 15610 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Details: DETAILS--TRNA COORDINATES (TRNA09) WERE FIT INTO CRYO-EM MAP AS RIGID BODIES THE RELATIVE POSITIONS OF THE TRNA IS DERIVED BY FITTING THE X-RAY STRUCTURE OF TRNA (TRNA09) INTO THE THREE- ...Details: DETAILS--TRNA COORDINATES (TRNA09) WERE FIT INTO CRYO-EM MAP AS RIGID BODIES THE RELATIVE POSITIONS OF THE TRNA IS DERIVED BY FITTING THE X-RAY STRUCTURE OF TRNA (TRNA09) INTO THE THREE-DIMENSIONAL CRYO-ELECTRON MICROSCOPY MAPS OF FUNCTIONAL COMPLEXES OF THE E. COLI 70S RIBOSOMES. IT SHOULD BE NOTED THAT ALL TRNA-BINDING POSITIONS ARE NOT OCCUPIED SIMULTANEOSLY. THEREFORE, THERE ARE OVERLAPS BETWEEN THE TWO TRNA COORDINATES. IN ORDER TO SEE THE RELATIVE POSITIONS OF VARIOUS RIBOSOMAL DOMAINS, CHAIN C (THE P-SITE TRNA) SHOULD BE ALIGNED WITH OUR EARLIER DEPOSITED P-SITE POSITION (ID CODE 1EGO).
RefinementHighest resolution: 17 Å
Refinement stepCycle: LAST / Highest resolution: 17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 8260 0 0 8260

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