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

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-0284
TitleMycobacterium smegmatis alternative protein ribosome (tRNA class 1)
Map dataClass 1 from focused classification with signal subtraction masking the tRNA binding sites
Sample
  • Complex: M.smegmatis cytosolic ribosome from Zn depleted cells binding alternative ribosomal proteins.
Biological speciesMycobacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsTobiasson V / Amunts A
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Zinc depletion does not necessarily induce ribosome hibernation in mycobacteria.
Authors: Victor Tobiasson / Allexa Dow / Sladjana Prisic / A Amunts /
History
DepositionOct 10, 2018-
Header (metadata) releaseJan 23, 2019-
Map releaseJan 23, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

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

emd_0284.png

Downloads & links

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Map

FileDownload / File: emd_0284.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationClass 1 from focused classification with signal subtraction masking the tRNA binding sites
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 350 pix.
= 290.5 Å		0.83 Å/pix.
x 350 pix.
= 290.5 Å		0.83 Å/pix.
x 350 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 LevelBy AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.009855312 - 0.031208888
Average (Standard dev.)0.00041037297 (±0.0030669007)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 290.5 Å
α=β=γ: 90.0 °

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
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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Half map: Class 1 from focused classification with signal subtraction...

Fileemd_0284_half_map_1.map
AnnotationClass 1 from focused classification with signal subtraction masking the tRNA binding sites HALF2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Class 1 from focused classification with signal subtraction...

Fileemd_0284_half_map_2.map
AnnotationClass 1 from focused classification with signal subtraction masking the tRNA binding sites HALF1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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.
Components
  • Complex: M.smegmatis cytosolic ribosome from Zn depleted cells binding alternative ribosomal proteins.

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Supramolecule #1: M.smegmatis cytosolic ribosome from Zn depleted cells binding alt...

SupramoleculeName: M.smegmatis cytosolic ribosome from Zn depleted cells binding alternative ribosomal proteins.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mycobacterium smegmatis (bacteria) / Location in cell: Cytoplasm

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Number grids imaged: 1 / Number real images: 2724 / Average exposure time: 6.0 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.8 µm / Calibrated defocus min: 0.6 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73485
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)

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