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- EMDB-1771: 30S Initiation Complex. 30S-IF1-IF2-IF3-tRNA-mRNA-GTP (after clas... -

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Basic information

Entry
Database: EMDB / ID: 1771
Title30S Initiation Complex. 30S-IF1-IF2-IF3-tRNA-mRNA-GTP (after classification)
Sample30S initiation complex
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map data30S initiation complex (after classification)
Methodsingle particle reconstruction, at 18.3 Å resolution
AuthorsJulian P / Milon P / Agirrezabala X / Lasso G / Gil D / Rodnina MV / Valle M
CitationPLoS Biol., 2011, 9, e1001095-e1001095

PLoS Biol., 2011, 9, e1001095-e1001095 Yorodumi Papers
The Cryo-EM structure of a complete 30S translation initiation complex from Escherichia coli.
Patricia Julián / Pohl Milon / Xabier Agirrezabala / Gorka Lasso / David Gil / Marina V Rodnina / Mikel Valle

DateDeposition: Aug 3, 2010 / Header (metadata) release: Sep 16, 2011 / Map release: Sep 16, 2011 / Last update: Dec 11, 2013

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.2
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_1771.map.gz (map file in CCP4 format, 8584 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
130 pix
2.8 Å/pix.
= 364. Å
130 pix
2.8 Å/pix.
= 364. Å
130 pix
2.8 Å/pix.
= 364. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.8 Å
Density
Contour Level:0.2 (by author), 0.2 (movie #1):
Minimum - Maximum-0.42882487 - 2.1288023
Average (Standard dev.)0.03256337 (0.15947002)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions130130130
Origin-65-65-65
Limit646464
Spacing130130130
CellA=B=C: 364 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z364.000364.000364.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-65-65-65
NC/NR/NS130130130
D min/max/mean-0.4292.1290.033

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Supplemental data

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Sample components

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Entire 30S initiation complex

EntireName: 30S initiation complex / Number of components: 1

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Component #1: ribosome-prokaryote, 30S initiation complex

Ribosome-prokaryoteName: 30S initiation complex / a.k.a: 30SIC / Prokaryote: SSU 30S / 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, 70 mM NH4Cl, 30 mM KCl, and 7 mM MgCl2
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 100 % / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderHolder: Cryo Specimen Holder / Model: GATAN LIQUID NITROGEN

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric)
3D reconstructionResolution: 18.3 Å / Resolution method: FSC 0.5

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