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- EMDB-5307: Three-dimensional cryo-electron microscopy density map of the 70S... -

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Basic information

Entry
Database: EMDB / ID: EMD-5307
TitleThree-dimensional cryo-electron microscopy density map of the 70S ribosome from Mycobacterium smegmatis
Map dataReconstruction of 70S ribosome from Mycobacterium smegmatis
Sample
  • Sample: 70S ribosome from Mycobacterium smegmatisRibosome
  • Complex: 70S ribosome with P-site tRNA
KeywordscryoEM / prokaryotic / ribosome / 3D-structure
Biological speciesMycobacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsShasmal M / Sengupta J
CitationJournal: PLoS One / Year: 2012
Title: Structural diversity in bacterial ribosomes: mycobacterial 70S ribosome structure reveals novel features.
Authors: Manidip Shasmal / Jayati Sengupta /
Abstract: Here we present analysis of a 3D cryo-EM map of the 70S ribosome from Mycobacterium smegmatis, a saprophytic cousin of the etiological agent of tuberculosis in humans, Mycobacterium tuberculosis. In ...Here we present analysis of a 3D cryo-EM map of the 70S ribosome from Mycobacterium smegmatis, a saprophytic cousin of the etiological agent of tuberculosis in humans, Mycobacterium tuberculosis. In comparison with the 3D structures of other prokaryotic ribosomes, the density map of the M. smegmatis 70S ribosome reveals unique structural features and their relative orientations in the ribosome. Dramatic changes in the periphery due to additional rRNA segments and extra domains of some of the peripheral ribosomal proteins like S3, S5, S16, L17, L25, are evident. One of the most notable features appears in the large subunit near L1 stalk as a long helical structure next to helix 54 of the 23S rRNA. The sharp upper end of this structure is located in the vicinity of the mRNA exit channel. Although the M. smegmatis 70S ribosome possesses conserved core structure of bacterial ribosome, the new structural features, unveiled in this study, demonstrates diversity in the 3D architecture of bacterial ribosomes. We postulate that the prominent helical structure related to the 23S rRNA actively participates in the mechanisms of translation in mycobacteria.
History
DepositionJun 9, 2011-
Header (metadata) releaseJun 27, 2011-
Map releaseJun 4, 2012-
UpdateMar 6, 2013-
Current statusMar 6, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 38
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 38
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5307_1.tif

Downloads & links

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Map

FileDownload / File: emd_5307.map.gz / Format: CCP4 / Size: 37 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of 70S ribosome from Mycobacterium smegmatis
Voxel sizeX=Y=Z: 1.69 Å
Density
Contour LevelBy AUTHOR: 38.0 / Movie #1: 38
Minimum - Maximum-151.530227660000008 - 292.594116209999981
Average (Standard dev.)4.70615911 (±27.37070847)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-106-106-106
Dimensions215215215
Spacing215215215
CellA=B=C: 363.35 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.691.691.69
M x/y/z215215215
origin x/y/z0.0000.0000.000
length x/y/z363.350363.350363.350
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-106-106-106
NC/NR/NS215215215
D min/max/mean-151.530292.5944.706

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Supplemental data

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Sample components

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Entire : 70S ribosome from Mycobacterium smegmatis

EntireName: 70S ribosome from Mycobacterium smegmatisRibosome
Components
  • Sample: 70S ribosome from Mycobacterium smegmatisRibosome
  • Complex: 70S ribosome with P-site tRNA

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Supramolecule #1000: 70S ribosome from Mycobacterium smegmatis

SupramoleculeName: 70S ribosome from Mycobacterium smegmatis / type: sample / ID: 1000 / Number unique components: 2
Molecular weightTheoretical: 2.5 MDa

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Supramolecule #1: 70S ribosome with P-site tRNA

SupramoleculeName: 70S ribosome with P-site tRNA / type: complex / ID: 1 / Name.synonym: 70S ribosome / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Mycobacterium smegmatis (bacteria)
Molecular weightTheoretical: 2.5 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: 20 mM Tris-HCl, pH 7.5, 10 mM magnesium acetate, 30 mM ammonium chloride, 5 mM 2-mercaptoethanol
GridDetails: Holey grid
VitrificationCryogen name: ETHANE / Chamber temperature: 94 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Cryo plunger. Rapid-freezing in liquid ethane

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 88466 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 89000
Sample stageSpecimen holder: Cryo transfer / Specimen holder model: GATAN LIQUID NITROGEN
DateNov 2, 2010
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Digitization - Sampling interval: 15 µm / Number real images: 269 / Average electron dose: 15 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: CTF correction of 3D map
Final reconstructionResolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 1

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Atomic model buiding 1

Initial modelPDB ID:

2i2u
PDB Unreleased entry

SoftwareName: PyMol
DetailsManual fitting
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 2

Initial modelPDB ID:

2i2v
PDB Unreleased entry

SoftwareName: PyMol
DetailsManual fitting
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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