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- EMDB-4933: Cryo-EM structure of the microsporidian ribosome: Multibody-refin... -

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Basic information

Entry
Database: EMDB / ID: EMD-4933
TitleCryo-EM structure of the microsporidian ribosome: Multibody-refined map body 3 (SSU-head)
Map data
SampleMicrosporidian Ribosome
Biological speciesVairimorpha necatrix (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsBarandun J / Hunziker M / Vossbrinck CR / Klinge S
Funding support United States, Switzerland, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences1DP2GM123459 United States
Swiss National Science Foundation155515 Switzerland
CitationJournal: Nat Microbiol / Year: 2019
Title: Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome.
Authors: Jonas Barandun / Mirjam Hunziker / Charles R Vossbrinck / Sebastian Klinge /
Abstract: Microsporidia are eukaryotic parasites that infect essentially all animal species, including many of agricultural importance, and are significant opportunistic parasites of humans. They are ...Microsporidia are eukaryotic parasites that infect essentially all animal species, including many of agricultural importance, and are significant opportunistic parasites of humans. They are characterized by having a specialized infection apparatus, an obligate intracellular lifestyle, rudimentary mitochondria and the smallest known eukaryotic genomes. Extreme genome compaction led to minimal gene sizes affecting even conserved ancient complexes such as the ribosome. In the present study, the cryo-electron microscopy structure of the ribosome from the microsporidium Vairimorpha necatrix is presented, which illustrates how genome compaction has resulted in the smallest known eukaryotic cytoplasmic ribosome. Selection pressure led to the loss of two ribosomal proteins and removal of essentially all eukaryote-specific ribosomal RNA (rRNA) expansion segments, reducing the rRNA to a functionally conserved core. The structure highlights how one microsporidia-specific and several repurposed existing ribosomal proteins compensate for the extensive rRNA reduction. The microsporidian ribosome is kept in an inactive state by two previously uncharacterized dormancy factors that specifically target the functionally important E-site, P-site and polypeptide exit tunnel. The present study illustrates the distinct effects of evolutionary pressure on RNA and protein-coding genes, provides a mechanism for ribosome inhibition and can serve as a structural basis for the development of inhibitors against microsporidian parasites.
History
DepositionMay 5, 2019-
Header (metadata) releaseJul 10, 2019-
Map releaseJul 10, 2019-
UpdateAug 7, 2019-
Current statusAug 7, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0136
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0136
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4933.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 340 pix.
= 408. Å
1.2 Å/pix.
x 340 pix.
= 408. Å
1.2 Å/pix.
x 340 pix.
= 408. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density
Contour LevelBy AUTHOR: 0.0136 / Movie #1: 0.0136
Minimum - Maximum-0.04515076 - 0.08667427
Average (Standard dev.)0.00009054843 (±0.001611273)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 408.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21.21.2
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z408.000408.000408.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-15-9-23
NX/NY/NZ635180
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.0450.0870.000

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Supplemental data

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Sample components

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Entire Microsporidian Ribosome

EntireName: Microsporidian Ribosome / Number of components: 1

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Component #1: protein, Microsporidian Ribosome

ProteinName: Microsporidian Ribosome / Recombinant expression: No
SourceSpecies: Vairimorpha necatrix (fungus)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 11 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 5.55 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Defocus: 500.0 - nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3284

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 333313
3D reconstructionSoftware: RELION / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 4V88

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