REL PDBe PDBe PDBe 2004-03-14 2004-03-15 2004-04-28 2012-10-31 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 E. coli ribosome translating GFP and tandem Ig domains - difference map E. coli ribosome translating GFP and tandem Ig domains - difference map
The sample was monodisperse.
2 tRNA molecules and the average of two nascent proteins 3 P site tRNA Escherichia coli OTHER SINGLE STRANDED false E site tRNA Escherichia coli OTHER SINGLE STRANDED false nascent protein Dictyostelium discoideum
Density for nascent protein is average of that for tandem Ig domains and GFP
1 monomer true Escherichia coli 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 50000.0 GATAN LIQUID NITROGEN 100 2000-05-02 KODAK SO-163 FILM OTHER 8.322
Scanner model: UMAX PowerLook 3000
5.0 8. Eucentric
Each negative dataset
 C1 OTHER 16.0 FSC 0.5 CUT-OFF SPIDER, IMAGIC, GAP, CNS, XPLOR
See entries 1068, 1070, 1071 and 1072. Vector difference maps were calculated between reconstructions of each nascent protein-ribosome complex and the control inactive map. The difference densities for the tandem Ig domains and GFP nascent proteins were more similar to each other than either was to the single Ig domain nascent protein. Therefore these two difference maps were averaged together to produce a set of consensus difference densities representing the main differences between inactive ribosomes and ribosomes stalled during translation that contain a nascent polypeptide chain.
SPIDER euler
 emd_1073.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 -319.889999999999986 325.819999999999993 -0.000938282 26.123799999999999 3.33 3.33 3.33 65.200000000000003 Average difference map calculated between individual difference maps for Ig2 and GFP ribosome-nascent chain complexes (see entries 1068, 1070, 1071, 1072).
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 RIGID BODY FIT GAP
Protocol: Rigid body
R-factor and correlation coefficient REAL