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Yorodumi- EMDB-4935: Evolutionary compaction and adaptation visualized by the structur... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4935 | |||||||||
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Title | Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome | |||||||||
Map data | Overall map, state1 | |||||||||
Sample |
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Keywords | Microsporidia / Ribosome / Intracellular Parasite | |||||||||
Biological species | Vairimorpha necatrix (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Barandun J / Hunziker M | |||||||||
Funding support | United States, Switzerland, 2 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4935.map.gz | 137.2 MB | EMDB map data format | |
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Header (meta data) | emd-4935-v30.xml emd-4935.xml | 89.2 KB 89.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4935_fsc.xml | 12.1 KB | Display | FSC data file |
Images | emd_4935.png | 270.4 KB | ||
Filedesc metadata | emd-4935.cif.gz | 17.6 KB | ||
Others | emd_4935_additional.map.gz | 137 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4935 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4935 | HTTPS FTP |
-Validation report
Summary document | emd_4935_validation.pdf.gz | 673.8 KB | Display | EMDB validaton report |
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Full document | emd_4935_full_validation.pdf.gz | 673.4 KB | Display | |
Data in XML | emd_4935_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | emd_4935_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4935 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4935 | HTTPS FTP |
-Related structure data
Related structure data | 6rm3MC 4931C 4932C 4933C 4934C C: citing same article (ref.) M: atomic model generated by this map |
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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
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4935.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Overall map, state1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Additional map, state2
File | emd_4935_additional.map | ||||||||||||
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Annotation | Additional map, state2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Microsporidian Ribosome
+Supramolecule #1: Microsporidian Ribosome
+Macromolecule #1: 16S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #78: 23S rRNA
+Macromolecule #3: uL2
+Macromolecule #4: uS2
+Macromolecule #5: uL15
+Macromolecule #6: eS26
+Macromolecule #7: uL3
+Macromolecule #8: eS1
+Macromolecule #9: eL29
+Macromolecule #10: eS27
+Macromolecule #11: uL4
+Macromolecule #12: uS5
+Macromolecule #13: eL30
+Macromolecule #14: eS28
+Macromolecule #15: uL18
+Macromolecule #16: uS3
+Macromolecule #17: eL31
+Macromolecule #18: uS14
+Macromolecule #19: eL6
+Macromolecule #20: eS4
+Macromolecule #21: eL32
+Macromolecule #22: eS30
+Macromolecule #23: uL30
+Macromolecule #24: uS7
+Macromolecule #25: eL33
+Macromolecule #26: eS31
+Macromolecule #27: eL8
+Macromolecule #28: eS6
+Macromolecule #29: eL34
+Macromolecule #30: RACK1
+Macromolecule #31: uL6
+Macromolecule #32: eS7
+Macromolecule #33: uL29
+Macromolecule #34: uL16
+Macromolecule #35: eS8
+Macromolecule #36: eL36
+Macromolecule #37: uL5
+Macromolecule #38: uS4
+Macromolecule #39: eL37
+Macromolecule #40: eL13
+Macromolecule #41: uS17
+Macromolecule #42: eL39
+Macromolecule #43: eL14
+Macromolecule #44: eL40
+Macromolecule #45: eS12
+Macromolecule #46: eL15
+Macromolecule #47: uS15
+Macromolecule #48: MDF2
+Macromolecule #49: MDF1
+Macromolecule #50: uL13
+Macromolecule #51: uS11
+Macromolecule #52: eL42
+Macromolecule #53: uL22
+Macromolecule #54: uS19
+Macromolecule #55: eL43
+Macromolecule #56: eL18
+Macromolecule #57: uS9
+Macromolecule #58: eL19
+Macromolecule #59: eS17
+Macromolecule #60: eL20
+Macromolecule #61: uS13
+Macromolecule #62: eL21
+Macromolecule #63: eS19
+Macromolecule #64: eL22
+Macromolecule #65: uS10
+Macromolecule #66: uL14
+Macromolecule #67: eS21
+Macromolecule #68: eL24
+Macromolecule #69: uS8
+Macromolecule #70: uL23
+Macromolecule #71: uS12
+Macromolecule #72: msL1
+Macromolecule #73: uL24
+Macromolecule #74: eS24
+Macromolecule #75: eL27
+Macromolecule #76: eS25
+Macromolecule #77: eS10
+Macromolecule #79: MAGNESIUM ION
+Macromolecule #80: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 11 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 50 mA | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film 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 beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus min: 4.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |