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Yorodumi- PDB-6rm3: Evolutionary compaction and adaptation visualized by the structur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rm3 | |||||||||
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Title | Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome | |||||||||
Components |
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Keywords | RIBOSOME / Microsporidia / Intracellular Parasite | |||||||||
Function / homology | RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) Function and homology information | |||||||||
Biological species | Vairimorpha necatrix (fungus) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Barandun, J. / Hunziker, M. / Vossbrinck, C.R. / Klinge, S. | |||||||||
Funding support | United States, Switzerland, 2items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6rm3.cif.gz | 3.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6rm3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6rm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rm3_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6rm3_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6rm3_validation.xml.gz | 314.7 KB | Display | |
Data in CIF | 6rm3_validation.cif.gz | 521.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rm/6rm3 ftp://data.pdbj.org/pub/pdb/validation_reports/rm/6rm3 | HTTPS FTP |
-Related structure data
Related structure data | 4935MC 4931C 4932C 4933C 4934C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | |
EM raw data | EMPIAR-11075 (Title: Single-particle cryo-EM dataset of the Vairimorpha necatrix ribosome Data size: 1.0 TB Data #1: Unaligned multi-frame micrographs of the Vairimorpha necatrix ribosome [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 3 types, 3 molecules S60L70L50
#1: RNA chain | Mass: 401303.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus) |
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#2: RNA chain | Mass: 38379.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus) |
#78: RNA chain | Mass: 799487.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus) |
+Protein , 75 types, 75 molecules LA0SA0LAASAALB0SB0LBBSBBLC0SC0LCCSCCLD0SD0LDDSDDLE0SE0LEESEELF0SF0LFFSFFLG0SG0LGGSGGLH0SH0...
-Non-polymers , 2 types, 183 molecules
#79: Chemical | ChemComp-MG / #80: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Microsporidian Ribosome / Type: COMPLEX / Entity ID: #1-#78 / Source: NATURAL | ||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) | Organism: Vairimorpha necatrix (fungus) | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 11 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Details: 50 mA / Grid material: COPPER / Grid mesh size: 400 divisions/in. | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus min: 500 nm / Calibrated defocus min: 4000 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 0.25 sec. / Electron dose: 5.55 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 3284 |
Image scans | Movie frames/image: 32 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 471121 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 185445 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4V88 Accession code: 4V88 / Source name: PDB / Type: experimental model |