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- EMDB-8626: Structure of the 30S subunit -

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Basic information

Entry
Database: EMDB / ID: 8626
TitleStructure of the 30S subunit
Sample30S Consensus subunit
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataStructure of the 30S subunit
Methodsingle particle reconstruction, at 6 Å resolution
AuthorsRazi A / Guarne A / Ortega J
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, E3396-E3403

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, E3396-E3403 Yorodumi Papers
The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly.
Aida Razi / Alba Guarné / Joaquin Ortega

DateDeposition: Feb 26, 2017 / Header (metadata) release: Mar 15, 2017 / Map release: Apr 19, 2017 / Last update: May 10, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0215
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 0.0215
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_8626.map.gz (map file in CCP4 format, 42593 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
220 pix
1.45 Å/pix.
= 319. Å
220 pix
1.45 Å/pix.
= 319. Å
220 pix
1.45 Å/pix.
= 319. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.45 Å
Density
Contour Level:0.0215 (by author), 0.0215 (movie #1):
Minimum - Maximum-0.031991478 - 0.10743945
Average (Standard dev.)0.0010633138 (0.0056903656)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions220220220
Origin000
Limit219219219
Spacing220220220
CellA=B=C: 319 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z319.000319.000319.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0320.1070.001

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Supplemental data

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Sample components

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Entire 30S Consensus subunit

EntireName: 30S Consensus subunit / Number of components: 1

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Component #1: protein, 30S Consensus subunit

ProteinName: 30S Consensus subunit / 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: 10 mM Tris-HCl at pH 7.5, 10 mM magnesium acetate, 150 mM NH4Cl, 3mM 2-mercaptoethanol and 2 mM GMP-PNP
pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 25000 X (nominal), 34482 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 3000 nm
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 142945
3D reconstructionSoftware: Relion / Resolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
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  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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