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- EMDB-0284: Mycobacterium smegmatis alternative protein ribosome (tRNA class 1) -

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Basic information

Entry
Database: EMDB / ID: 0284
TitleMycobacterium smegmatis alternative protein ribosome (tRNA class 1)
Map dataClass 1 from focused classification with signal subtraction masking the tRNA binding sites
SampleM.smegmatis cytosolic ribosome from Zn depleted cells binding alternative ribosomal proteins.:
SourceMycobacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / 4.5 Å resolution
AuthorsTobiasson V / Amunts A
CitationJournal: To Be Published
Title: Cryo-EM structure of Mycobacterium smegmatis ribosome from zinc depleted cells.
Authors: Tobiasson V / Dow A / Prisic S / Amunts A
DateDeposition: Oct 10, 2018 / Header (metadata) release: Jan 23, 2019 / Map release: Jan 23, 2019 / Last update: Jan 23, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0284.png

Downloads & links

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Map

Fileemd_0284.map.gz (map file in CCP4 format, 171501 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
350 pix
0.83 Å/pix.
= 290.5 Å		350 pix
0.83 Å/pix.
= 290.5 Å		350 pix
0.83 Å/pix.
= 290.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour Level:0.006 (by author), 0.006 (movie #1):
Minimum - Maximum-0.009855312 - 0.031208888
Average (Standard dev.)0.00041037297 (0.0030669007)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions350350350
Origin0.00.00.0
Limit349.0349.0349.0
Spacing350350350
CellA=B=C: 290.5 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z290.500290.500290.500
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.0100.0310.000

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Supplemental data

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Sample components

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Entire M.smegmatis cytosolic ribosome from Zn depleted cells binding alt...

EntireName: M.smegmatis cytosolic ribosome from Zn depleted cells binding alternative ribosomal proteins.
Number of components: 1

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Component #1: protein, M.smegmatis cytosolic ribosome from Zn depleted cells bi...

ProteinName: M.smegmatis cytosolic ribosome from Zn depleted cells binding alternative ribosomal proteins.
Recombinant expression: No
SourceSpecies: Mycobacterium smegmatis (bacteria)
Source (natural)Location in cell: Cytoplasm

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Experimental details

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Sample preparation

SpecimenSpecimen state: cell / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 3 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 800.0 - 2400.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 BASE (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2724

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 73485
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF

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