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- EMDB-13680: Cryo-EM structure of small subunit of Giardia lamblia ribosome at... -
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Open data
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Basic information
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Title | Cryo-EM structure of small subunit of Giardia lamblia ribosome at 2.9 A resolution | |||||||||
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![]() | ribosome / giardia / parasite | |||||||||
Function / homology | ![]() endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.85 Å | |||||||||
![]() | Hiregange DG / Rivalta A / Bose T / Breiner-Goldstein E / Samiya S / Cimicata G / Kulakova L / Zimmerman E / Bashan A / Herzberg O / Yonath A | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of the ancient eukaryotic ribosome from the human parasite Giardia lamblia. Authors: Disha-Gajanan Hiregange / Andre Rivalta / Tanaya Bose / Elinor Breiner-Goldstein / Sarit Samiya / Giuseppe Cimicata / Liudmila Kulakova / Ella Zimmerman / Anat Bashan / Osnat Herzberg / Ada Yonath / ![]() ![]() Abstract: Giardiasis is a disease caused by the protist Giardia lamblia. As no human vaccines have been approved so far against it, and resistance to current drugs is spreading, new strategies for combating ...Giardiasis is a disease caused by the protist Giardia lamblia. As no human vaccines have been approved so far against it, and resistance to current drugs is spreading, new strategies for combating giardiasis need to be developed. The G. lamblia ribosome may provide a promising therapeutic target due to its distinct sequence differences from ribosomes of most eukaryotes and prokaryotes. Here, we report the cryo-electron microscopy structure of the G. lamblia (WB strain) ribosome determined at 2.75 Å resolution. The ribosomal RNA is the shortest known among eukaryotes, and lacks nearly all the eukaryote-specific ribosomal RNA expansion segments. In contrast, the ribosomal proteins are typically eukaryotic with some species-specific insertions/extensions. Most typical inter-subunit bridges are maintained except for one missing contact site. Unique structural features are located mainly at the ribosome's periphery. These may be exploited as target sites for the design of new compounds that inhibit selectively the parasite's ribosomal activity. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 37.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 44.4 KB 44.4 KB | Display Display | ![]() |
Images | ![]() | 48.6 KB | ||
Filedesc metadata | ![]() | 10.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 431.5 KB | Display | ![]() |
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Full document | ![]() | 431.1 KB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Data in CIF | ![]() | 8.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pwfMC ![]() 7pwgC ![]() 7pwoC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Giardia lamblia small subunit
+Supramolecule #1: Giardia lamblia small subunit
+Macromolecule #1: Ribosomal protein S29A
+Macromolecule #2: Ribosomal protein S19e
+Macromolecule #3: Ribosomal protein S13
+Macromolecule #4: Ribosomal protein S9
+Macromolecule #5: Ribosomal protein S3
+Macromolecule #6: Ribosomal protein S23
+Macromolecule #7: Ribosomal protein S18
+Macromolecule #8: Ribosomal protein S16
+Macromolecule #9: Ribosomal protein S2
+Macromolecule #10: 40S ribosomal protein SA
+Macromolecule #11: 40S ribosomal protein S3a
+Macromolecule #12: Ribosomal protein S24
+Macromolecule #13: Ribosomal protein S27
+Macromolecule #14: 40S ribosomal protein S26
+Macromolecule #15: 40S ribosomal protein S25
+Macromolecule #16: 40S ribosomal protein S21
+Macromolecule #17: Ribosomal protein S15
+Macromolecule #18: Ribosomal protein S17
+Macromolecule #19: Ribosomal protein S10B
+Macromolecule #20: 40S ribosomal protein S8
+Macromolecule #21: 40S ribosomal protein S30
+Macromolecule #22: Ribosomal protein eS7
+Macromolecule #23: Ribosomal protein eL41
+Macromolecule #24: Ribosomal protein S28
+Macromolecule #25: Ribosomal protein S14
+Macromolecule #26: Ribosomal protein S15A
+Macromolecule #27: 40S ribosomal protein S4
+Macromolecule #29: SSU ribosomal protein S17P
+Macromolecule #30: Ribosomal protein S20
+Macromolecule #31: 40S ribosomal protein S6
+Macromolecule #32: Ribosomal protein S5
+Macromolecule #28: rRNA 18S
+Macromolecule #33: POTASSIUM ION
+Macromolecule #34: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 91058 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |