+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3844 | |||||||||
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Title | 80S from Trypanosoma cruzi | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information translation regulator activity / phosphorylation / ribosome binding / kinase activity / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome ...translation regulator activity / phosphorylation / ribosome binding / kinase activity / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / RNA binding / zinc ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Trypanosoma cruzi (eukaryote) / Trypanosoma cruzi (strain CL Brener) (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Brito Querido J / Mancera-Martinez E / Vicens Q / Bochler A / Chicher J / Simonetti A / Hashem Y | |||||||||
Citation | Journal: Structure / Year: 2017 Title: The cryo-EM Structure of a Novel 40S Kinetoplastid-Specific Ribosomal Protein. Authors: Jailson Brito Querido / Eder Mancera-Martínez / Quentin Vicens / Anthony Bochler / Johana Chicher / Angelita Simonetti / Yaser Hashem / Abstract: Kinetoplastids are potentially lethal protozoan pathogens affecting more than 20 million people worldwide. There is a critical need for more specific targets for the development of safer anti- ...Kinetoplastids are potentially lethal protozoan pathogens affecting more than 20 million people worldwide. There is a critical need for more specific targets for the development of safer anti-kinetoplastid therapeutic molecules that can replace the scarce and highly cytotoxic current drugs. The kinetoplastid ribosome represents a potential therapeutic target due to its relative structural divergence when compared with its human counterpart. However, several kinetoplastid-specific ribosomal features remain uncharacterized. Here, we present the near-atomic cryoelectron microscopy structure of a novel bona fide kinetoplastid-specific ribosomal (r-) protein (KSRP) bound to the ribosome. KSRP is an essential protein located at the solvent face of the 40S subunit, where it binds and stabilizes kinetoplastid-specific domains of rRNA, suggesting its role in ribosome integrity. KSRP also interacts with the r-protein eS6 at a region that is only conserved in kinetoplastids. The kinetoplastid-specific ribosomal environment of KSRP provides a promising target for the design of safer anti-kinetoplastidian drugs. | |||||||||
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_3844.map.gz | 117.1 MB | EMDB map data format | |
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Header (meta data) | emd-3844-v30.xml emd-3844.xml | 51.2 KB 51.2 KB | Display Display | EMDB header |
Images | emd_3844.png | 70.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3844 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3844 | HTTPS FTP |
-Validation report
Summary document | emd_3844_validation.pdf.gz | 328.1 KB | Display | EMDB validaton report |
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Full document | emd_3844_full_validation.pdf.gz | 327.2 KB | Display | |
Data in XML | emd_3844_validation.xml.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3844 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3844 | HTTPS FTP |
-Related structure data
Related structure data | 5optMC 3845C 5osgC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3844.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.56 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : 80S ribosome from Trypanosoma cruzi
+Supramolecule #1: 80S ribosome from Trypanosoma cruzi
+Macromolecule #1: Activated protein kinase C receptor, putative
+Macromolecule #2: Ribosomal protein S29, putative
+Macromolecule #3: 40S ribosomal protein S16, putative
+Macromolecule #4: 40S ribosomal protein S15, putative
+Macromolecule #5: 40S ribosomal protein S18, putative
+Macromolecule #6: 40S ribosomal protein S4
+Macromolecule #7: 40S ribosomal protein S23, putative
+Macromolecule #8: 40S ribosomal protein S5, putative
+Macromolecule #9: Ribosomal protein S7, putative
+Macromolecule #10: 40S ribosomal protein S13, putative
+Macromolecule #11: 40S ribosomal protein S27, putative
+Macromolecule #12: 40S ribosomal protein S26
+Macromolecule #13: 40S ribosomal protein S33, putative
+Macromolecule #14: 40S ribosomal protein S14, putative
+Macromolecule #15: 40S ribosomal protein S3a-2
+Macromolecule #16: 40S ribosomal protein S11, putative
+Macromolecule #17: 40S ribosomal protein S24
+Macromolecule #18: 40S ribosomal protein S8
+Macromolecule #19: 40S ribosomal protein S9, putative
+Macromolecule #20: 40S ribosomal protein SA
+Macromolecule #21: 40S ribosomal protein S2, putative
+Macromolecule #22: 40S ribosomal protein S15a, putative
+Macromolecule #23: 40S ribosomal protein S21, putative
+Macromolecule #24: Ribosomal protein S25, putative
+Macromolecule #25: 40S ribosomal protein S12
+Macromolecule #26: Ubiquitin/ribosomal protein S27a, putative
+Macromolecule #27: 40S ribosomal protein S6
+Macromolecule #28: 40S ribosomal protein S17, putative
+Macromolecule #29: Ribosomal protein S20, putative
+Macromolecule #30: 40S ribosomal protein S3, putative
+Macromolecule #31: 40S ribosomal protein S10, putative
+Macromolecule #32: Ribosomal protein S19, putative
+Macromolecule #33: 40S ribosomal protein S30
+Macromolecule #34: RNA-binding protein, putative
+Macromolecule #35: 18S rRNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 2.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 86000 |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |