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- EMDB-23076: Mycobacterium smegmatis 70S-MPY complex at high resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-23076
TitleMycobacterium smegmatis 70S-MPY complex at high resolution
Map dataMycobacterium smegmatis 70S-MPY complex at high resolution
Sample
  • Complex: Human mitochondrial ribosome-EF-G1 complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSharma MR / Koripella RK / Agrawal RK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01 GM61576 United States
CitationJournal: Microbiology (Reading) / Year: 2021
Title: Ribosome hibernation: a new molecular framework for targeting nonreplicating persisters of mycobacteria.
Authors: Yunlong Li / Manjuli R Sharma / Ravi K Koripella / Nilesh K Banavali / Rajendra K Agrawal / Anil K Ojha /
Abstract: Treatment of tuberculosis requires a multi-drug regimen administered for at least 6 months. The long-term chemotherapy is attributed in part to a minor subpopulation of nonreplicating cells that ...Treatment of tuberculosis requires a multi-drug regimen administered for at least 6 months. The long-term chemotherapy is attributed in part to a minor subpopulation of nonreplicating cells that exhibit phenotypic tolerance to antibiotics. The origins of these cells in infected hosts remain unclear. Here we discuss some recent evidence supporting the hypothesis that hibernation of ribosomes in induced by zinc starvation, could be one of the primary mechanisms driving the development of nonreplicating persisters in hosts. We further analyse inconsistencies in previously reported studies to clarify the molecular principles underlying mycobacterial ribosome hibernation.
History
DepositionDec 7, 2020-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateMar 15, 2023-
Current statusMar 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23076.png

Downloads & links

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Map

FileDownload / File: emd_23076.map.gz / Format: CCP4 / Size: 357 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMycobacterium smegmatis 70S-MPY complex at high resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 454 pix.
= 485.78 Å		1.07 Å/pix.
x 454 pix.
= 485.78 Å		1.07 Å/pix.
x 454 pix.
= 485.78 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45 / Movie #1: 0.45
Minimum - Maximum-1.6641397 - 3.4974866
Average (Standard dev.)0.0027263619 (±0.13195492)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions454454454
Spacing454454454
CellA=B=C: 485.78003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z454454454
origin x/y/z0.0000.0000.000
length x/y/z485.780485.780485.780
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ500500500
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS454454454
D min/max/mean-1.6643.4970.003

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Supplemental data

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Sample components

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Entire : Human mitochondrial ribosome-EF-G1 complex

EntireName: Human mitochondrial ribosome-EF-G1 complex
Components
  • Complex: Human mitochondrial ribosome-EF-G1 complex

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Supramolecule #1: Human mitochondrial ribosome-EF-G1 complex

SupramoleculeName: Human mitochondrial ribosome-EF-G1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#88
Source (natural)Organism: Homo sapiens (human)

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 69.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66840
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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