REL RCSB RCSB RCSB 2008-12-01 2009-02-25 2009-05-05 2014-07-23 Aminoacyl-tRNA-EF-Tu-GDP-kir ternary complex-bound E. coli 70S ribosome Villa E Sengupta J Trabuco LG LeBarron J Baxter WT Shaikh TR Grassucci RA Nissen P Ehrenberg M Schulten K Frank J decoding, tRNA selection, GTPase, accommodation, flexible fitting, cryo-EM, MDFF, hydrophobic gate, EF-Tu, ribosome, ternary complex Villa E Sengupta J Trabuco LG LeBarron J Baxter WT Shaikh TR Grassucci RA Nissen P Ehrenberg M Schulten K Frank J Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. PROC.NAT.ACAD.SCI.USA 106 1063 1068 2009 19122150 doi:10.1073/pnas.0811370106 LeBarron J Grassucci RA Shaikh TR Baxter WT Sengupta J Frank J Exploration of parameters in cryo-EM leading to an improved density map of the E.coli ribosome J.STRUCT.BIOL. 164 24 32 2008 18606549 doi:10.1016/j.jsb.2008.05.007 Trabuco LG Villa E Mitra K Frank J Schulten K Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. STRUCTURE (LONDON) 16 673 683 2008 18462672 doi:10.1016/j.str.2008.03.005 4v69 FULLOVERLAP 70S ribosome from E. coli complex 70S-fMet-tRNA-Phe-tRNA-EF-Tu-GDP-kirromycin. 70S ribosome from E. coli complex 70S-fMet-tRNA-Phe-tRNA-EF-Tu-GDP-kirromycin. single particle 5 70S ribosome false Escherichia coli ribosome-prokaryote: ALL fMet-tRNAfMet Escherichia coli TRANSFER SINGLE STRANDED false Phe-tRNAPhe Escherichia coli TRANSFER SINGLE STRANDED false tRNA Escherichia coli TRANSFER SINGLE STRANDED false Elongation factor Tu Escherichia coli cytoplasm
EF-Tu bound to kirromycin and GDP
1 monomer true Escherichia coli singleParticle particle 0.0768 7.5
5 mM potassium phosphate, 5 mM magnesium acetate, 5 mM ammonium chloride, 95 mM potassium chloride, 0.5 mM calcium chloride, 8 mM putrescine, 1 mM spermidine, and 1 mM dithioerythritol
Thin Carbon on 300 mesh Quantifoil R2/4
 ETHANE 90 80 OTHER
Vitrification instrument: FEI vitrobot. Blot Offset at -1 mm
Blot 3 seconds before plunging FEI POLARA 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.26 1.2 4.52 59000.0 58279.0 OTHER 84 Objective lens astigmatism was corrected at 115,000 times magnification with fastscan ccd
Low dose
2006-08-31 KODAK SO-163 FILM ZEISS SCAI 7 304 20 1.2 12. FEI Polara Cartridge
Correction of reconstruction of each defocus group
 OTHER 6.7 OTHER Spider 131599 emd_5036.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 309 309 309 -155 -155 -155 309 309 309 370.80002 370.80002 370.80002 90.0 90.0 90.0 X Y Z -114.578193659999997 303.004394530000013 6.03115606 29.14512062 1.2 1.2 1.2 90.0 AUTHOR Ternary complex-bound 70S E. coli ribosome
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 2I2U FLEXIBLE FIT MDFF
Protocol: MDFF. An atomic model of the entire ribosome and factors was creating using molecular dynamics flexible fitting (Trabuco et al. Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics. Structure (2008) vol. 16 (5) pp. 673-683)
RMSD, cross correlation REAL 2I2V FLEXIBLE FIT MDFF
Protocol: MDFF. An atomic model of the entire ribosome and factors was creating using molecular dynamics flexible fitting (Trabuco et al. Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics. Structure (2008) vol. 16 (5) pp. 673-683)
RMSD, cross correlation REAL 1OB2 FLEXIBLE FIT MDFF
Protocol: MDFF. An atomic model of the entire ribosome and factors was creating using molecular dynamics flexible fitting (Trabuco et al. Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics. Structure (2008) vol. 16 (5) pp. 673-683)
RMSD, cross correlation REAL