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Title:A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting.
Authors:O.Namy, S.J.Moran, D.I.Stuart, R.J.C.Gilbert, I.Brierley
Sample:Rabbit reticuloyte ribosome stalled on IBV mRNA containing pseudoknot with tRNA and eEF2
Aggregation state:Single particle (16.2 angstroms resolution)
Red flagLatest update:2011-09-02
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bullet_white.gif  Summary
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bullet.png Experimental details
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bullet_white.gif  Visualization
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Sample
Sample name: Rabbit reticuloyte ribosome stalled on IBV mRNA containing pseudoknot with tRNA and eEF2
Oligomeric state: One each of 40S, 60S, mRNA, eEF2 and P-site tRNA
Theoretical molecular weight of the sample: 3.5
Components:
ID Type Name Exp. MW (MDa) Oligomeric details Recombinant expression Synthetic Organism GO identifier InterPro identifier Virus identifier Details
1ribosome-eukaryoteSmall subunit
2ribosome-eukaryoteLarge subunit
3nucleic-acidMessage with pseudoknotfalseInfectious bronchitis virus
4proteinElongation translocaseMonomerfalseOryctolagus cuniculus
5nucleic-acidP-site transfer RNAfalseOryctolagus cuniculus
Experiment
Sample preparation:
pHSample conc.DetailsStainingSample support details
mg/mL300 mesh gold w/ lacey carbon
Vitrification:
Cryogen nameHumidityTemp.Instr.MethodTime resolvedDetails
ETHANE% K ms
Imaging:
MicroscopeVoltageIllumination modeImaging modeCsDefocus min.Defocus max.Nominal mag.Calibrated mag.Electron sourceDetectorDetector distanceAstigmatism
FEI/PHILIPS CM200FEG200 kVSPOT SCANBRIGHT FIELD2 mm1000 nm7000 nm50000FIELD EMISSION GUNKodak SO163 film mm

Specimen holderHolder modelTilt min.Tilt max.Energy filterEnergy windowTemp.Temp. min.Temp. max.Beam tiltElectron doseOther detailsDate
EucentricGATAN LIQUID NITROGEN°° eV100 K K K mrad2 e/Å2
Processing
Software:SPIDER and GAP
CTF correction:By micrograph
Resolution by author:16.2 Å
Resolution method:FSC at 0.5 cut-off
Processing details:Deposited map is composite of computationally-separated subunits and bound co-factors from the final map.
Unit cell:
Scanned images:
Num. imagesSampling sizeOD rangeQuant. bit numberOther detailsScanner
313.33 μm/pixel58linkOTHER
Fitting:
PDBProtocolTarget crit.SoftwareB valueFitting spacePDB chainDetails
Rigid bodyCCURODomains manually docked in O and refined in URO
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