REL PDBe PDBe PDBe 2004-03-14 2004-03-14 2004-04-28 2014-12-10 Three-dimensional structures of translating ribosomes by Cryo-EM. Gilbert RJC Fucini P Connell S Fuller SD Nierhaus KH Robinson CV Dobson CM Stuart DI Gilbert RJ Fucini P Connell S Fuller SD Nierhaus KH Robinson CV Dobson CM Stuart DI Three-dimensional structures of translating ribosomes by Cryo-EM. MOLECULAR CELL 14 57 66 2004 15068803 doi:10.1016/S1097-2765(04)00163-7 70S E. coli ribosome translating 1 Ig domain 70S E. coli ribosome translating 1 Ig domain
The sample was monodisperse.
30S subunit and 50S subunit, 2 tRNA molecules and 1 Ig nascent polypeptide 5 E. coli 30S subunit false Escherichia coli ribosome-prokaryote: SSU 30S E. coli 50S subunit false Escherichia coli ribosome-prokaryote: LSU 50S P site tRNA Escherichia coli
partial occupancy
OTHER SINGLE STRANDED false E site tRNA Escherichia coli
partial occupancy lower than P site
OTHER SINGLE STRANDED false Ig domain of D. discoideum ABP Dictyostelium discoideum Slime mould 1 Monomer true In vitro transcription.translation system pT7-7 singleParticle particle 5.0
20 mM HEPES, 150 mM ammonium acetate, 6 mM magnesium acetate, 2 mM spermidine, 0.05 mM spermine and 4 mM 2-mercaptoethanol. Concentration of ribosomes expressed to A260 units.
300 mesh copper grid with holey carbon film
 ETHANE 100 HOMEMADE PLUNGER
Vitrification instrument: Standard unmodified guillotine plunger
 FEI/PHILIPS CM200FEG OTHER OTHER FIELD EMISSION GUN 200 2 1.295 4.655 50000.0 GATAN LIQUID NITROGEN 100 2000-05-01 KODAK SO-163 FILM ZEISS SCAI 7 20 5.0 8. Eucentric
Each negative dataset
 C1 OTHER 13.4 FSC 0.5 CUT-OFF SPIDER, IMAGIC, GAP, CNS, XPLOR
Final maps were calculated from 8032 images from a total of 28928 from 20 individual datasets, with scaling in reciprocal space to crystallographic ribosome structures and correction for map anisotropy by B-factor weighting of amplitudes in XPLOR with respect to a similarly-treated control inactive ribosome. Selection of particles for inclusion in the final maps was by correlation coefficient with respect to the alignment model, designed to maximise nascent chain occupancy in the selected images.
8032
SPIDER euler
 emd_1070.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 426.24 426.24 426.24 90 90 90 Z X Y -2.23039 3.96822 0.000000000035653 0.453244 3.33 3.33 3.33 1.13 3D reconstruction of an E. coli ribosome stalled in translating an immunoglobulin domain from the Actin Binding Protein of Dictyostelium discoideum
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 RIGID BODY FIT GAP
Protocol: Rigid body
R-factor and correlation coefficient REAL