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- EMDB-1311: Cryo-EM visualization of transfer messenger RNA with two SmpBs in... -

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Basic information

Entry
Database: EMDB / ID: 1311
TitleCryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome.
SampleThermus thermophilus 70S ribosome
SourceThermus thermophilus / bacteria / thermophilic / tRNA / サームス・サーモフィラス
Map dataCryo-EM map of Thermus thermophilus 70S ribosome bound with tmRNA, two small protein B, and EF-Tu in the presence of S1 in solution.
Methodsingle particle reconstruction, at 13.6 A resolution
AuthorsKaur S / Gillet R / Li W / Gursky R / Frank J
CitationProc. Natl. Acad. Sci. U.S.A., 2006, 103, 16484-16489

Proc. Natl. Acad. Sci. U.S.A., 2006, 103, 16484-16489 StrPapers
Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome.
Sukhjit Kaur / Reynald Gillet / Wen Li / Richard Gursky / Joachim Frank

DateDeposition: Dec 13, 2006 / Header (metadata) release: Dec 14, 2006 / Map release: Dec 14, 2006 / Last update: Dec 13, 2006

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 30.915807559
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 30.915807559
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_1311.map.gz (map file in CCP4 format, 8584 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
130 pix
2.82 A/pix
= 366.6 A
130 pix
2.82 A/pix
= 366.6 A
130 pix
2.82 A/pix
= 366.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.82 A
Density
Contour Level:73.2, 30.9158076 (movie #1):
Minimum - Maximum-117.854 - 304.088
Average (Standard dev.)6.06499 (30.402)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions130130130
Origin-65-65-65
Limit646464
Spacing130130130
CellA=B=C: 366.6 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.822.822.82
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z366.600366.600366.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-63-63-63
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-65-65-65
NC/NR/NS130130130
D min/max/mean-117.854304.0886.065

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Supplemental data

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Sample components

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Entire Thermus thermophilus 70S ribosome

EntireName: Thermus thermophilus 70S ribosome / Number of components: 5
MassTheoretical: 2.4 MDa

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Component #1: ribosome-prokaryote, 70S Ribosome

Ribosome-prokaryoteName: 70S Ribosome / Prokaryote: ALL
MassExperimental: 2.3 MDa

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Component #2: protein, small protein B

ProteinName: small protein B / Recombinant expression: No / Number of Copies: 2
MassExperimental: 19 kDa
SourceSpecies: Thermus thermophilus / bacteria / thermophilic / サームス・サーモフィラス

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Component #3: nucleic-acid, tmRNA

Nucleic-acidName: tmRNA / Class: RNA / Structure: OTHER / Synthetic: No
SourceSpecies: Thermus thermophilus / bacteria / thermophilic / サームス・サーモフィラス

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Component #4: nucleic-acid, tRNA

Nucleic-acidName: tRNA / Class: T-RNA / Structure: OTHER / Synthetic: No
SourceSpecies: Thermus thermophilus / bacteria / thermophilic / tRNA / サームス・サーモフィラス

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Component #5: protein, EF-Tu

ProteinName: EF-Tu / Number of Copies: 1 / Recombinant expression: No
SourceSpecies: Thermus thermophilus / bacteria / thermophilic / サームス・サーモフィラス

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: see Methods / pH: 7.5
Support filmQuanti-foil grids coated with a thin carbon layer
StainingNo staining (Cryo-EM)
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 279 K / Humidity: 80 %
Method: Blot for 5 seconds before plunging Rapid plunge freezing in liquid ethane
Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20 / Date: Aug 13, 2004
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM
LensMagnification: 5000 X (nominal), 49696 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1475 - 3635 nm
Specimen HolderHolder: cryo transfer / Model: GATAN LIQUID NITROGEN / Temperature: 93 K ( 93 - 93 K)
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 27 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 8

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 52829 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Back projection / Software: SPIDER package / CTF correction: CTF correctionn of 3D map / Resolution: 13.6 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: O / Refinement protocol: rigid body / Details: Protocol: Rigid Body. manual fitting with O
Output model

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