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- EMDB-5595: Structure of the immature 30S subunit from a Escherichia coli rim... -

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Basic information

Entry
Database: EMDB / ID: EMD-5595
TitleStructure of the immature 30S subunit from a Escherichia coli rimM null strain. Conformation 1.
Map dataStructure of an immature 30S subunit from an E. coli rimM null strain. Conformation 1
Sample
  • Sample: Structure of an immature 30S subunit from an E. coli rimM null strain. Conformation 1
  • Complex: ribosome 30S subunit
KeywordsRibosome assembly / 30S subunit / RimM protein
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 17.0 Å
AuthorsLeong V / Kent M / Jomaa A / Ortega J
CitationJournal: RNA / Year: 2013
Title: Escherichia coli rimM and yjeQ null strains accumulate immature 30S subunits of similar structure and protein complement.
Authors: Leong V / Kent M / Jomaa A / Ortega J
History
DepositionMar 6, 2013-
Header (metadata) releaseMar 20, 2013-
Map releaseMay 8, 2013-
UpdateMay 29, 2013-
Current statusMay 29, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5595.tif

Downloads & links

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Map

FileDownload / File: emd_5595.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of an immature 30S subunit from an E. coli rimM null strain. Conformation 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.54 Å/pix.
x 128 pix.
= 325.12 Å		2.54 Å/pix.
x 128 pix.
= 325.12 Å		2.54 Å/pix.
x 128 pix.
= 325.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.54 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-4.79457808 - 17.30347252
Average (Standard dev.)0.0 (±0.99285036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 325.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.542.542.54
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z325.120325.120325.120
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-4.79517.303-0.000

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Supplemental data

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Sample components

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Entire : Structure of an immature 30S subunit from an E. coli rimM null st...

EntireName: Structure of an immature 30S subunit from an E. coli rimM null strain. Conformation 1
Components
  • Sample: Structure of an immature 30S subunit from an E. coli rimM null strain. Conformation 1
  • Complex: ribosome 30S subunit

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Supramolecule #1000: Structure of an immature 30S subunit from an E. coli rimM null st...

SupramoleculeName: Structure of an immature 30S subunit from an E. coli rimM null strain. Conformation 1
type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1
Molecular weightExperimental: 930 KDa / Theoretical: 930 KDa

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Supramolecule #1: ribosome 30S subunit

SupramoleculeName: ribosome 30S subunit / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: SSU 30S, PSR16s
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BW25113 / Location in cell: cytoplasm
Molecular weightExperimental: 930 KDa / Theoretical: 930 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Details: 10 mM Tris-HCl, pH 7.5, 10 mM Mg acetate, 60 mM NH4Cl and 3 mM 2-mercaptoethanol
GridDetails: 400 mesh cupped grid with thin carbon support, glow discharged in air
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: FEI VITROBOT MARK III / Method: Blot twice for 7 seconds each.

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Electron microscopy

MicroscopeJEOL 2010F
TemperatureAverage: 97 K
DateJul 10, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 250 / Average electron dose: 15 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Liquid nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsReconstruction obtained with Xmipp package
CTF correctionDetails: CTFFIND
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Xmipp / Number images used: 18966

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