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- EMDB-5909: Cryo-EM structure of high salt treated immature 30S ribosomal sub... -

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Basic information

Entry
Database: EMDB / ID: 5909
TitleCryo-EM structure of high 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 high 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 / 15.2 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 13, 2014 / Header (metadata) release: Mar 12, 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: 2.96
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2.96
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_5909.map.gz (map file in CCP4 format, 7815 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
126 pix
2.62 Å/pix.
= 330.12 Å
126 pix
2.62 Å/pix.
= 330.12 Å
126 pix
2.62 Å/pix.
= 330.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.62 Å
Density
Contour Level:2.96 (by author), 2.96 (movie #1):
Minimum - Maximum-2.60272765 - 13.71421242
Average (Standard dev.)0E-8 (0.99999976)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions126126126
Origin-62-62-62
Limit636363
Spacing126126126
CellA=B=C: 330.12 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.622.622.62
M x/y/z126126126
origin x/y/z0.0000.0000.000
length x/y/z330.120330.120330.120
α/β/γ90.00090.00090.000
start NX/NY/NZ-95-75153
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-62-62-62
NC/NR/NS126126126
D min/max/mean-2.60313.7140.000

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Supplemental data

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Sample components

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Entire Cryo-EM structure of high salt treated immature 30S ribosomal sub...

EntireName: Cryo-EM structure of high 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, high salt treated immature 30S ribosomal sub...

Ribosome-prokaryoteName: high 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: 10mM Tris-HCl, 60mM NH4Cl,10mM MgCl2, 0.1mM EDTA,1mM DTT
pH: 7.8
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: Nov 7, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 700 - 5200 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI EAGLE (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 23956 / Details: this is a classification volume using RELION
3D reconstructionAlgorithm: reference projection / Software: SPIDER / CTF correction: weiner filter / Resolution: 15.2 Å / Resolution method: FSC 0.5, semi-independent

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