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Yorodumi- PDB-7ase: 43S preinitiation complex from Trypanosoma cruzi with the kDDX60 ... -
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-Basic information
Entry | Database: PDB / ID: 7ase | |||||||||||||||
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Title | 43S preinitiation complex from Trypanosoma cruzi with the kDDX60 helicase | |||||||||||||||
Components |
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Keywords | TRANSLATION / preinitiation / factors / kinetoplastid / helicase | |||||||||||||||
Function / homology | Function and homology information : / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / translation regulator activity / translation initiation factor binding / translation initiation factor activity ...: / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / translation regulator activity / translation initiation factor binding / translation initiation factor activity / ribosomal small subunit assembly / metallopeptidase activity / cytosolic small ribosomal subunit / ribosome binding / small ribosomal subunit / kinase activity / tRNA binding / nucleic acid binding / membrane => GO:0016020 / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / phosphorylation / GTPase activity / GTP binding / RNA binding / zinc ion binding / ATP binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Trypanosoma cruzi (eukaryote) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å | |||||||||||||||
Authors | Bochler, A. / Brito Querido, J. / Prilepskaja, T. / Soufari, H. / Del Cistia, M.L. / Kuhn, L. / Rimoldi Ribeiro, A. / Valasek, L.S. / Hashem, Y. | |||||||||||||||
Funding support | France, Czech Republic, 4items
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Citation | Journal: Cell Rep / Year: 2020 Title: Structural Differences in Translation Initiation between Pathogenic Trypanosomatids and Their Mammalian Hosts. Authors: Anthony Bochler / Jailson Brito Querido / Terezie Prilepskaja / Heddy Soufari / Angelita Simonetti / Mayara Lucia Del Cistia / Lauriane Kuhn / Aline Rimoldi Ribeiro / Leoš Shivaya Valášek / Yaser Hashem / Abstract: Canonical mRNA translation in eukaryotes begins with the formation of the 43S pre-initiation complex (PIC). Its assembly requires binding of initiator Met-tRNA and several eukaryotic initiation ...Canonical mRNA translation in eukaryotes begins with the formation of the 43S pre-initiation complex (PIC). Its assembly requires binding of initiator Met-tRNA and several eukaryotic initiation factors (eIFs) to the small ribosomal subunit (40S). Compared to their mammalian hosts, trypanosomatids present significant structural differences in their 40S, suggesting substantial variability in translation initiation. Here, we determine the structure of the 43S PIC from Trypanosoma cruzi, the parasite causing Chagas disease. Our structure shows numerous specific features, such as the variant eIF3 structure and its unique interactions with the large rRNA expansion segments (ESs) 9, 7, and 6, and the association of a kinetoplastid-specific DDX60-like helicase. It also reveals the 40S-binding site of the eIF5 C-terminal domain and structures of key terminal tails of several conserved eIFs underlying their activities within the PIC. Our results are corroborated by glutathione S-transferase (GST) pull-down assays in both human and T. cruzi and mass spectrometry data. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 7ase.cif.gz | 3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7ase.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ase.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/7ase ftp://data.pdbj.org/pub/pdb/validation_reports/as/7ase | HTTPS FTP |
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-Related structure data
Related structure data | 11893MC 7askC 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 , 12 types, 12 molecules fsjnpJVwGK8H
#1: Protein | Mass: 246749.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4E5Z1 |
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#5: Protein | Mass: 47700.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4E620 |
#6: Protein | Mass: 16624.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: A0A2V2VP49 |
#7: Protein | Mass: 38227.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DH88 |
#8: Protein | Mass: 35070.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DTN2 |
#26: Protein | Mass: 27676.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DY32 |
#37: Protein | Mass: 12577.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DM75 |
#38: Protein | Mass: 18418.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: A0A2V2WGW5 |
#43: Protein | Mass: 38589.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DQZ2 |
#44: Protein | Mass: 22458.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DDK1 |
#47: Protein | Mass: 87439.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DL69 |
#50: Protein | Mass: 38408.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DSJ1 |
-RNA chain , 2 types, 2 molecules 10
#2: RNA chain | Mass: 24255.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) |
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#3: RNA chain | Mass: 746696.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: GenBank: 320364483 |
+40S ribosomal protein ... , 26 types, 26 molecules yrumZoqRStUvXFdahPiMNbcTWl
-Putative 40S ribosomal protein ... , 2 types, 2 molecules Bg
#21: Protein | Mass: 22180.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: A0A2V2WBN2 |
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#24: Protein | Mass: 27634.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: A0A2V2UKQ3 |
-Eukaryotic translation initiation factor ... , 6 types, 6 molecules 5EYCIA
#28: Protein | Mass: 52642.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4CPV7 |
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#39: Protein | Mass: 46320.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4D7F2 |
#40: Protein | Mass: 42887.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DZB0 |
#46: Protein | Mass: 82331.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4E3G1 |
#49: Protein | Mass: 56331.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4D5W3 |
#51: Protein | Mass: 57492.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DCN0 |
-Ribosomal protein ... , 3 types, 3 molecules LOQ
#31: Protein | Mass: 13248.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4D6H7 |
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#34: Protein | Mass: 18861.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DJY1 |
#41: Protein | Mass: 6651.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4CXR4 |
-Protein/peptide , 1 types, 1 molecules D
#42: Protein/peptide | Mass: 4348.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: G0U1J3 |
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-Non-polymers , 3 types, 3 molecules
#53: Chemical | ChemComp-ZN / |
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#54: Chemical | ChemComp-MG / |
#55: Chemical | ChemComp-GNP / |
-Details
Has ligand of interest | N |
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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: 43S preinitiation complex from Trypanosoma cruzi with the helicase kDDX60 Type: COMPLEX / Entity ID: #1-#52 / Source: NATURAL |
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Source (natural) | Organism: Trypanosoma cruzi (eukaryote) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-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: OTHER |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33775 / Symmetry type: POINT |