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- EMDB-1122: Visualizing tmRNA entry into a stalled ribosome. -

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Basic information

Entry
Database: EMDB / ID: 1122
TitleVisualizing tmRNA entry into a stalled ribosome.
Sample70S-Psite tRNA - mRNA - EF-Tu.GDP - alanylated tmRNA - SmpB - Kirromycin - S1
SourceThermus thermophilus hb8 / bacteria / thermophilic
Map datathis is a ribosome consisting 70S + Psite tRNA + mRNA + EF-Tu.GDP + alanylated tmRNA + SmpB + Kirromycin + S1
Methodsingle particle reconstruction, at 13 A resolution
AuthorsValle M / Gillet R / Kaur S / Henne A / Ramakrishnan V / Frank J
CitationScience, 2003, 300, 127-130

Science, 2003, 300, 127-130 StrPapers
Visualizing tmRNA entry into a stalled ribosome.
Mikel Valle / Reynald Gillet / Sukhjit Kaur / Anke Henne / V Ramakrishnan / Joachim Frank

DateDeposition: Mar 24, 2005 / Header (metadata) release: Apr 11, 2005 / Map release: Apr 11, 2005 / Last update: Mar 24, 2005

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 42
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 42
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-1zc8
  • Surface level: 42
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1122.map.gz (map file in CCP4 format, 10720 KB)
Projections & slices
Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
140 pix
2.82 A/pix
= 394.8 A
140 pix
2.82 A/pix
= 394.8 A
140 pix
2.82 A/pix
= 394.8 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:54.9, 42 (movie #1):
Minimum - Maximum-147.485 - 313.886
Average (Standard dev.)2.87458 (28.7702)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions140140140
Origin-70-70-70
Limit696969
Spacing140140140
CellA=B=C: 394.8 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.822.822.82
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z394.800394.800394.800
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-220-220-220
NX/NY/NZ441441441
MAP C/R/S123
start NC/NR/NS-70-70-70
NC/NR/NS140140140
D min/max/mean-147.485313.8862.875

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Supplemental data

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Sample components

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Entire 70S-Psite tRNA - mRNA - EF-Tu.GDP - alanylated tmRNA - SmpB - Kir...

EntireName: 70S-Psite tRNA - mRNA - EF-Tu.GDP - alanylated tmRNA - SmpB - Kirromycin - S1
Number of components: 5

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Component #1: ribosome-prokaryote, 70S Ribosome

Ribosome-prokaryoteName: 70S Ribosome / Details: Thermus thermophilus / Prokaryote: ALL / Recombinant expression: No
SourceSpecies: Thermus thermophilus hb8 / bacteria / thermophilic

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Component #2: nucleic-acid, tRNA

Nucleic-acidName: tRNA / Class: T-RNA / Details: P site / Structure: SINGLE STRANDED / Synthetic: No
SourceSpecies: Thermus thermophilus hb8 / bacteria / thermophilic

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Component #3: protein, EF-Tu

ProteinName: EF-Tu / Recombinant expression: No
SourceSpecies: Thermus thermophilus hb8 / bacteria / thermophilic

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Component #4: ligand, tmRNA

LigandName: tmRNA / Recombinant expression: No
SourceSpecies: Thermus thermophilus hb8 / bacteria / thermophilic

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Component #5: protein, SmpB

ProteinName: SmpB / Recombinant expression: No
SourceSpecies: Thermus thermophilus hb8 / bacteria / thermophilic

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 25 mM Hepes-KOH pH 7.5, 30 mM NH4Cl, 7mM MgCl2, 2 mM ATP, 6 mM PEP, 10g/ml PK
pH: 7.5
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 93 K / Humidity: 90 % / Method: Blot for 2 seconds before plunging
Details: Vitrification instrument: two side blotting plunger

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20 / Date: Aug 1, 2002
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 49000 X (nominal), 52000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1450 - 3700 nm
Specimen HolderHolder: Cryo transfer / Model: GATAN LIQUID NITROGEN / Temperature: 93 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 44 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 12 / OD range: 1.2

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 27644 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: reference projection / Software: SPIDER / CTF correction: defocus groups / Resolution: 13 A / Resolution method: FSC at 0.15 cut-off / Euler angles: SPIDER definition

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Atomic model buiding

Modeling #1Software: manual / Refinement protocol: rigid body / Target criteria: cross correlation coefficient
Details: Protocol: Rigid Body. The domains were separately fitted by manual docking using program O
Output model

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