+Open data
-Basic information
Entry | Database: PDB / ID: 5opt | |||||||||
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Title | Structure of KSRP in context of Trypanosoma cruzi 40S | |||||||||
Components |
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Keywords | RIBOSOME / Kinetoplastids / cryo-EM / KSRP | |||||||||
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) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | |||||||||
Authors | Brito Querido, J. / Mancera-Martinez, E. / Vicens, Q. / Bochler, A. / Chicher, J. / Simonetti, A. / Hashem, Y. | |||||||||
Funding support | France, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5opt.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5opt.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 5opt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5opt_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5opt_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 5opt_validation.xml.gz | 192.2 KB | Display | |
Data in CIF | 5opt_validation.cif.gz | 312.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/5opt ftp://data.pdbj.org/pub/pdb/validation_reports/op/5opt | HTTPS FTP |
-Related structure data
Related structure data | 3844MC 3845C 5osgC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 3 molecules pjh
#1: Protein | Mass: 35070.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote) Strain: CL Brener / Gene: Tc00.1047053511211.120, Tc00.1047053511211.130 / Production host: Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DTN2 |
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#26: Protein | Mass: 16608.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote) Strain: CL Brener / Gene: Tc00.1047053510409.39 / Production host: Trypanosoma cruzi (eukaryote) / References: UniProt: Q4D1T6 |
#34: Protein | Mass: 27676.303 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote) Strain: CL Brener / Gene: Tc00.1047053511727.270 / Production host: Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DY32 |
-Ribosomal protein ... , 5 types, 5 molecules qQalo
#2: Protein | Mass: 6651.826 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote) Strain: CL Brener Gene: Tc00.1047053506025.14, Tc00.1047053511209.54, Tc00.1047053511805.15 Production host: Trypanosoma cruzi (eukaryote) / References: UniProt: Q4CXR4 |
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#9: Protein | Mass: 24896.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote) Strain: CL Brener / Gene: Tc00.1047053506593.30 / Production host: Trypanosoma cruzi (eukaryote) / References: UniProt: Q4CUC7 |
#24: Protein | Mass: 12379.955 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote) Strain: CL Brener / Gene: Tc00.1047053504105.94, Tc00.1047053509233.190 / Production host: Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DTX6 |
#29: Protein | Mass: 13248.478 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote) Strain: CL Brener Gene: Tc00.1047053508475.10, Tc00.1047053508823.120, Tc00.1047053508823.140 Production host: Trypanosoma cruzi (eukaryote) / References: UniProt: Q4D6H7 |
#32: Protein | Mass: 18861.287 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote) Strain: CL Brener / Gene: Tc00.1047053510879.20 / Production host: Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DJY1 |
+40S ribosomal protein ... , 26 types, 26 molecules rtuLMORSTUVWXYZbfdegiPkmnc
-RNA chain , 1 types, 1 molecules E
#35: RNA chain | Mass: 746696.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Trypanosoma cruzi (eukaryote) / References: GenBank: 320364483 |
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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: 80S ribosome from Trypanosoma cruzi / Type: RIBOSOME / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Trypanosoma cruzi (eukaryote) |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 2.2 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86000 / Symmetry type: POINT |