Journal: 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
Deposition
Jul 19, 2000
Deposition site: RCSB / Processing site: RCSB
Revision 1.0
Aug 11, 2000
Provider: repository / Type: Initial release
Revision 1.1
Apr 27, 2008
Group: Version format compliance
Revision 1.2
Jul 13, 2011
Group: Non-polymer description / Version format compliance
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Crystal grow
*PLUS
Method: other / Details: electron microscopy
-
Electron microscopy imaging
Microscopy
Model: FEI/PHILIPS EM420
Electron gun
Electron source: OTHER / Illumination mode: FLOOD BEAM
Electron lens
Mode: BRIGHT FIELD / Nominal magnification: 52200 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Specimen holder
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recording
Electron dose: 10 e/Å2 / Film or detector model: GENERIC FILM
Image scans
Scanner model: PERKIN ELMER
-
Processing
Symmetry
Point symmetry: C1 (asymmetric)
3D reconstruction
Resolution: 17 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Num. of particles: 15610 / Symmetry type: POINT
Atomic model building
Space: 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).
Refinement
Highest resolution: 17 Å
Refinement step
Cycle: LAST / Highest resolution: 17 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
0
8260
0
0
8260
+
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