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- EMDB-5792: Cryo-electron microscopy of an immature 50S ribosomal subunit (45... -

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Basic information

Entry
Database: EMDB / ID: EMD-5792
TitleCryo-electron microscopy of an immature 50S ribosomal subunit (45S particle) from Bacillus subtilis depleted of RbgA (YlqF), conformation 4
Map data3D reconstruction of an immature 50S ribosomal subunit (45S particle) from Bacillus subtilis depleted of RbgA (YlqF), conformation 4
Sample
  • Sample: Immature 50S ribosomal subunit (45S particle) from Bacillus subtilis depleted of RbgA (YlqF), conformation 4
  • Complex: 45S particle
KeywordsRibosome assembly / 50S subunit / RbgA / YlqF / GTPase / 45S subunit
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.0 Å
AuthorsJomaa A / Jain N / Davis JH / Williamson JR / Britton RA / Ortega J
CitationJournal: NUCLEIC ACIDS RES. / Year: 2014
Title: Functional domains of the 50S subunit mature late in the assembly process.
Authors: Jomaa A / Jain N / Davis JH / Williamson JR / Britton RA / Ortega J
History
DepositionNov 10, 2013-
Header (metadata) releaseDec 25, 2013-
Map releaseJan 8, 2014-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing 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
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  • Surface view colored by height
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_5792.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of an immature 50S ribosomal subunit (45S particle) from Bacillus subtilis depleted of RbgA (YlqF), conformation 4
Voxel sizeX=Y=Z: 2.54 Å
Density
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-6.91481352 - 12.08916664
Average (Standard dev.)0.0 (±1.0)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-6.91512.0890.000

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Supplemental data

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Sample components

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Entire : Immature 50S ribosomal subunit (45S particle) from Bacillus subti...

EntireName: Immature 50S ribosomal subunit (45S particle) from Bacillus subtilis depleted of RbgA (YlqF), conformation 4
Components
  • Sample: Immature 50S ribosomal subunit (45S particle) from Bacillus subtilis depleted of RbgA (YlqF), conformation 4
  • Complex: 45S particle

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Supramolecule #1000: Immature 50S ribosomal subunit (45S particle) from Bacillus subti...

SupramoleculeName: Immature 50S ribosomal subunit (45S particle) from Bacillus subtilis depleted of RbgA (YlqF), conformation 4
type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 1.6 MDa

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Supramolecule #1: 45S particle

SupramoleculeName: 45S particle / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI
Ribosome-details: ribosome-prokaryote: LSU 50S, LSU RNA 23S, LSU RNA 5S
Source (natural)Organism: Bacillus subtilis (bacteria) / Strain: RB301 / Location in cell: cytoplasm
Molecular weightTheoretical: 1.6 MDa

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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 magnesium acetate, 60 mM ammonium chloride, 3 mM 2-mercaptoethanol
GridDetails: 400 mesh holey carbon grids with an additional layer (5-10 nm) of thin carbon. Grids were glow discharged at 5 mA for 15 seconds.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: FEI VITROBOT MARK III
Method: Grids were blotted twice, for 7 seconds each time, before being plunged into liquid ethane.

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Electron microscopy

MicroscopeJEOL 2010F
TemperatureMin: 77 K / Max: 77 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 300,000 times magnification
DateFeb 1, 2012
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 12.7 µm / Number real images: 300 / Average electron dose: 20 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: 3.9 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Gatan 914 cryo-holder / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: ctFFIND
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: OTHER / Software - Name: Xmipp / Number images used: 23715

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