REL PDBe PDBe PDBe 2009-12-17 2010-04-09 2010-04-09 2010-04-09 Structure of a rabbit ribosome with an A-P'' hybrid state tRNA Flanagan IV JF Namy O Brierley I Gilbert RJC Ribosome,mRNA,tRNA,pseudoknot,hybrid state Flanagan JF Namy O Brierley I Gilbert RJ Direct observation of distinct A/P hybrid-state tRNAs in translocating ribosomes. STRUCTURE 18 257 264 2010 20159470 doi:10.1016/j.str.2009.12.007 Rabbit reticulocyte ribosome stalled on a pseudoknot-containing mRNA with an A-P'' hybrid-state tRNA Rabbit reticulocyte ribosome stalled on a pseudoknot-containing mRNA with an A-P'' hybrid-state tRNA Ribosome, mRNA, tRNA 3 80S ribosome
The sample was purified by affinity chromatography using a tagged mRNA.
1 40S and 60S false Oryctolagus cuniculus Rabbit Reticulocyte tRNA Oryctolagus cuniculus Rabbit TRANSFER OTHER false Infectious bronchitis virus mRNA Infectious bronchitis virus OTHER SINGLE STRANDED true singleParticle particle 7.8
25mM Hepes-KOH pH 7.8, 5mM MgOAc, 1mM cycloheximide, 150mM KOAc
300 mesh copper grid with lacey carbon film
 ETHANE 100 HOMEMADE PLUNGER
Vitrification instrument: Homemade plunger
Blot with Whatman number 1 paper FEI TECNAI F30 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2 0.92 5.3 38000.0 GATAN LIQUID NITROGEN 115 At 200,000 magnification KODAK SO-163 FILM ZEISS SCAI 7 107 8. Eucentric
Per micrograph
 C1 OTHER 14.9 FSC 0.5 CUT-OFF Spider, WellMAP
Maps were calculated using 24494 out of 64413 particles selected by the A-P-state tRNA. Presence of the tRNA was proved using multivariate statistical analysis focused classification of particles without previous alignment to a tRNA-containing ribosome.
24494
Spider convention
 emd_1672.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 X Y Z -98.5 202.030000000000001 2.37506 12.634 3.33 3.33 3.33 17.0 AUTHOR This is a reconstruction of a rabbit reticulocyte ribosome stalled on a pseudoknot-containing mRNA with a distorted A-P'' hybrid state tRNA.
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 2ZKQ RIGID BODY FIT URO
Protocol: Rigid body in segments. Subregions were defined as described in the paper accompanying this deposition.
Correlation coefficient RECIPROCAL 1evv RIGID BODY FIT URO, Refmac, NMFF
Protocol: Rigid body, Refmac and normal modes fitting. The tRNA crystal structure was regularisaed in Refmac (CCP4) and then subjected to normal modes-assisted flexible fitting using the program NMFF (Tama et al.)
REAL 2ZKR RIGID BODY FIT URO
Protocol: Rigid body in segments. Subregions were defined as described in the paper accompanying this deposition.
Correlation coefficient RECIPROCAL