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- EMDB-1553: Pretranslocation ribosome. Group after ML3D classification. Rache... -

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Basic information

Entry
Database: EMDB / ID: 1553
TitlePretranslocation ribosome. Group after ML3D classification. Racheted ribosome with tRNAs in hybrid positions.
Keywordsribosome / pretranslocation / hybrid
Sample70 mRNA tRNAfMet fMetLeu-tRNALeu
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataRacheted ribosome with tRNAs in hybrid positions.
Methodsingle particle reconstruction, at 16 Å resolution
AuthorsJulian P / Konevega AL / Scheres SHW / Lazaro M / Gil D / Wintermeyer W / Rodnina MV / Valle M
CitationProc. Natl. Acad. Sci. U.S.A., 2008, 105, 16924-16927

Proc. Natl. Acad. Sci. U.S.A., 2008, 105, 16924-16927 Yorodumi Papers
Structure of ratcheted ribosomes with tRNAs in hybrid states.
Patricia Julián / Andrey L Konevega / Sjors H W Scheres / Melisa Lázaro / David Gil / Wolfgang Wintermeyer / Marina V Rodnina / Mikel Valle

DateDeposition: Sep 8, 2008 / Header (metadata) release: Sep 15, 2008 / Map release: May 5, 2009 / Last update: Oct 24, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 32
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 32
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1553.map.gz (map file in CCP4 format, 16001 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
2.2 Å/pix.
= 352. Å
160 pix
2.2 Å/pix.
= 352. Å
160 pix
2.2 Å/pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.2 Å
Density
Contour Level:32 (by author), 32 (movie #1):
Minimum - Maximum-81.066 - 192.719
Average (Standard dev.)3.9672 (24.5844)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin-80-80-80
Limit797979
Spacing160160160
CellA=B=C: 352 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z352.000352.000352.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-81-81-81
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
D min/max/mean-81.066192.7193.967

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Supplemental data

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Sample components

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Entire 70 mRNA tRNAfMet fMetLeu-tRNALeu

EntireName: 70 mRNA tRNAfMet fMetLeu-tRNALeu / Number of components: 3

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Component #1: ribosome-prokaryote, 70S E.coli ribosome in the pretranslocation state

Ribosome-prokaryoteName: 70S E.coli ribosome in the pretranslocation state / a.k.a: pretranslocation ribosome / Prokaryote: ALL / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 50 mM Tris-HCl, pH 7.5 30mM KCl 70 mM NH4Cl 20 mM MgCl2 2 mM spermine
pH: 7.5
Support filmQuantifoil 300 mesh copper
StainingcryoEM
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 100 % / Method: single blot for 1.5 seconds / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderHolder: single tilt cryoholder / Model: GATAN LIQUID NITROGEN / Temperature: 90 K
CameraDetector: GENERIC GATAN

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Image acquisition

Image acquisitionSampling size: 2.2 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 12590 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: reference matching / Software: SPIDER XMIPP / CTF correction: volume / Details: subset after ML3D classification / Resolution: 16 Å / Resolution method: FSC at 0.15 cut-off

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