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- EMDB-5904: Cryo-EM structure of low salt treated immature 30S ribosomal subu... -

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Entry
Database: EMDB / ID: 5904
TitleCryo-EM structure of low salt treated immature 30S ribosomal subunit from rsga and rbfa deleted E.coli strain
Map datathe map is normalized to N(0,1)
SampleCryo-EM structure of low salt treated immature 30S ribosomal subunit from rsga and rbfa deleted E.coli strain:
ribosome-prokaryote
Keywords30S subunit assembly / RsgA / RbfA / 17S rRNA processing
SourceEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / negative staining / 13.5 Å resolution
AuthorsYang Z / Guo Q / Goto S / Chen Y / Li N / Yan K / Zhang Y / Muto A / Deng H / Himeno H / Lei J / Gao N
CitationJournal: Protein Cell / Year: 2014
Title: Structural insights into the assembly of the 30S ribosomal subunit in vivo: functional role of S5 and location of the 17S rRNA precursor sequence.
Authors: Zhixiu Yang / Qiang Guo / Simon Goto / Yuling Chen / Ningning Li / Kaige Yan / Yixiao Zhang / Akira Muto / Haiteng Deng / Hyouta Himeno / Jianlin Lei / Ning Gao
DateDeposition: Feb 12, 2014 / Header (metadata) release: Mar 5, 2014 / Map release: Apr 9, 2014 / Last update: Jun 11, 2014

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.48
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2.48
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_5904.map.gz (map file in CCP4 format, 7449 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
124 pix
3 Å/pix.
= 372. Å
124 pix
3 Å/pix.
= 372. Å
124 pix
3 Å/pix.
= 372. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3 Å
Density
Contour Level:2.48 (by author), 2.48 (movie #1):
Minimum - Maximum-2.77118325 - 12.55140114
Average (Standard dev.)0E-8 (0.99999976)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions124124124
Origin-61-61-61
Limit626262
Spacing124124124
CellA=B=C: 372.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z333
M x/y/z124124124
origin x/y/z0.0000.0000.000
length x/y/z372.000372.000372.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-95-75153
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-61-61-61
NC/NR/NS124124124
D min/max/mean-2.77112.5510.000

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Supplemental data

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Sample components

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Entire Cryo-EM structure of low salt treated immature 30S ribosomal subu...

EntireName: Cryo-EM structure of low salt treated immature 30S ribosomal subunit from rsga and rbfa deleted E.coli strain
Number of components: 1
MassTheoretical: 800 kDa / Experimental: 800 kDa

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Component #1: ribosome-prokaryote, low salt treated immature 30S ribosomal subu...

Ribosome-prokaryoteName: low salt treated immature 30S ribosomal subunit from rsga and rbfa deleted E.coli strain
a.k.a: immature 30S / Prokaryote: SSU 30S / Recombinant expression: No
MassTheoretical: 800 kDa / Experimental: 800 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: A19

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining, cryo EM
Sample solutionBuffer solution: 20mM Tris-HCl, 150mM NH4Cl,10mM Mg(OAc)2 / pH: 7.5
Support filmQuantifoil 2/4 grids were coated with carbon and glow discharged in a Harrick Plasma Cleaner for 30 seconds
Staininggrids were prepared with an FEI Vitrobot Mark IV
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Method: blot for 1 second before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Jul 14, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 8500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI EAGLE (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 4365

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 46414
Details: this is a classification volume (NO.2 of five groups) using RELION
3D reconstructionAlgorithm: reference projection / Software: SPIDER / CTF correction: weiner filter / Resolution: 13.5 Å / Resolution method: FSC 0.5, semi-independent

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