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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 dataCryo-EM structure of the microsporidian ribosome: Multibody-refined map body 3 (SSU-head)
Sample
  • Complex: Microsporidian 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-
UpdateNov 6, 2019-
Current statusNov 6, 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

emd_4933.png

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)
AnnotationCryo-EM structure of the microsporidian ribosome: Multibody-refined map body 3 (SSU-head)
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

Histogram

Histogram (log scale)
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
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
Components
  • Complex: Microsporidian Ribosome

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Supramolecule #1: Microsporidian Ribosome

SupramoleculeName: Microsporidian Ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#78
Source (natural)Organism: Vairimorpha necatrix (fungus)

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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

Concentration11 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
30.0 mMTris-HCL
5.0 mMMgOAc
25.0 mMKCl
1.0 mMDTT
1.0 mMEDTA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 2 / Number real images: 3284 / Average exposure time: 0.25 sec. / Average electron dose: 5.55 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 4.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 471121
CTF correctionSoftware - Name: RELION (ver. 3)
Startup modelType of model: INSILICO MODEL / In silico model: cryoSPARC generated initial model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 333313
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 2 / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4v88

RefinementSpace: REAL / Protocol: OTHER

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