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Title:Structure of the 39S Large Subunit of the Mammalian Mitochondrial Ribosome
Authors:Greber BJ, Boehringer D, Leitner A, Bieri P, Voigts-Hoffmann F, Erzberger JP, Leibundgut M, Aebersold R, Ban N
Sample:39S large subunit of the porcine mitochondrial ribosome
Method:Single particle reconstruction (4.9 angstroms resolution)
Red flagLatest update:2014-01-22
Sample
Sample name: 39S large subunit of the porcine mitochondrial ribosome
Oligomeric state: monomer
Theoretical molecular weight of the sample: 1.6
Components:
ID Type Name Exp. MW (MDa) Theo. MW (MDa) Oligomeric details Recombinant expression Synthetic Organism UniProt identifier GO identifier InterPro identifier Virus identifier Details
1cellular-component39S large subunit of the mitochondrial ribosome1.6MonomerfalseSus scrofa domesticusGO:0005761
Experiment
Specimen state: Particle
Specimen preparation:
pHSpecimen conc.DetailsStainingSpecimen support details
7.9 mg/mL20 mM HEPES-KOH, 100 mM KCl, 1 mM DTT, 20 mM MgCl2200 mesh Quantifoil R2/1 and R 2/2 holey carbon grids
Vitrification:
Cryogen nameHumidityTemp.Instr.MethodTime resolvedDetails
ETHANE% KHOMEMADE PLUNGER ms
Imaging:
MicroscopeVoltageIllumination modeImaging modeCsDefocus min.Defocus max.Nominal mag.Calibrated mag.Electron sourceDetectorDetector distanceAstigmatism
FEI TITAN KRIOS300 kVFLOOD BEAMBRIGHT FIELD2.7 mm1500 nm3300 nm75000141510FIELD EMISSION GUNFEI FALCON I (4k x 4k) mm
FEI TITAN KRIOS300 kVFLOOD BEAMBRIGHT FIELD2.7 mm1200 nm3600 nm5900099290FIELD EMISSION GUNFEI FALCON I (4k x 4k) mm
FEI TITAN KRIOS300 kVFLOOD BEAMBRIGHT FIELD2.7 mm1200 nm3600 nm5900099290FIELD EMISSION GUNFEI FALCON I (4k x 4k) mm
FEI TITAN KRIOS300 kVFLOOD BEAMBRIGHT FIELD2.7 mm1200 nm3600 nm5900099290FIELD EMISSION GUNFEI FALCON I (4k x 4k) mm
FEI TITAN KRIOS300 kVFLOOD BEAMBRIGHT FIELD2.7 mm1200 nm3600 nm5900099290FIELD EMISSION GUNFEI FALCON I (4k x 4k) mm
FEI TITAN KRIOS300 kVFLOOD BEAMBRIGHT FIELD2.7 mm1200 nm3600 nm5900099290FIELD EMISSION GUNFEI FALCON I (4k x 4k) mm
FEI TITAN KRIOS300 kVFLOOD BEAMBRIGHT FIELD2.7 mm1200 nm3600 nm5900099290FIELD EMISSION GUNFEI FALCON I (4k x 4k) mm
FEI TITAN KRIOS300 kVFLOOD BEAMBRIGHT FIELD2.7 mm1200 nm3600 nm5900099290FIELD EMISSION GUNFEI FALCON I (4k x 4k) mm

Specimen holderHolder modelTilt min.Tilt max.Energy filterEnergy windowTemp.Temp. min.Temp. max.Beam tiltElectron doseOther detailsDate
FEI TITAN KRIOS AUTOGRID HOLDER°° eV K K K mrad20 e/Å221-JUN-2013
FEI TITAN KRIOS AUTOGRID HOLDER°° eV K K K mrad20 e/Å202-MAY-2013
FEI TITAN KRIOS AUTOGRID HOLDER°° eV K K K mrad20 e/Å215-APR-2013
FEI TITAN KRIOS AUTOGRID HOLDER°° eV K K K mrad20 e/Å217-MAR-2013
FEI TITAN KRIOS AUTOGRID HOLDER°° eV K K K mrad20 e/Å219-FEB-2013
FEI TITAN KRIOS AUTOGRID HOLDER°° eV K K K mrad20 e/Å221-JAN-2013
FEI TITAN KRIOS AUTOGRID HOLDER°° eV K K K mrad20 e/Å219-DEC-2012
FEI TITAN KRIOS AUTOGRID HOLDER°° eV K K K mrad20 e/Å230-NOV-2012
Processing
Protocol:projection matching
Software:Spider, IMAGIC-5, CTFFIND3, RELION
CTF correction:per detector frame
Number of particles:232181
Imposed symmetry:C1
Resolution by author:4.9 Å
Resolution method:FSC at 0.143 from 2 independently refined data half sets, gold-standard
Processing details:An initial reconstruction was obtained using the angular reconstitution approach in Imagic-5. For visualization purposes the final map was amplitude and MTF-corrected in RELION. Particles were selected and extracted in batchboxer (EMAN 1.9).
Scanned images:
Num. imagesSampling sizeOD rangeQuant. bit numberOther detailsScanner
14 μm/pixelFor data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Fitting:
PDBProtocolTarget crit.SoftwareB valueFitting spacePDB chainDetails
3V2D rigid bodyChimera, O, COOTREALRibosomal proteins and rRNA were docked into the density using Chimera. Individual domains were manually fitted an rebuild using COOT and O.