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Yorodumi- EMDB-11893: 43S preinitiation complex from Trypanosoma cruzi with the kDDX60 ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11893 | |||||||||||||||
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Title | 43S preinitiation complex from Trypanosoma cruzi with the kDDX60 helicase | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | preinitiation / factors / kinetoplastid / helicase / TRANSLATION | |||||||||||||||
Function / homology | Function and homology information eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity ...eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / 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) / translation initiation factor binding / translation initiation factor activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / modification-dependent protein catabolic process / protein tag activity / rRNA processing / metallopeptidase activity / ribosomal small subunit biogenesis / ribosome binding / kinase activity / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / nucleic acid binding / tRNA binding / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / nucleotide binding / ubiquitin protein ligase binding / GTP binding / RNA binding / zinc ion binding / ATP binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Trypanosoma cruzi (eukaryote) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.33 Å | |||||||||||||||
Authors | Bochler A / Brito Querido J | |||||||||||||||
Funding support | France, Czech Republic, 4 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11893.map.gz | 228.3 MB | EMDB map data format | |
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Header (meta data) | emd-11893-v30.xml emd-11893.xml | 70 KB 70 KB | Display Display | EMDB header |
Images | emd_11893.png | 77.8 KB | ||
Filedesc metadata | emd-11893.cif.gz | 17.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11893 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11893 | HTTPS FTP |
-Validation report
Summary document | emd_11893_validation.pdf.gz | 702.4 KB | Display | EMDB validaton report |
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Full document | emd_11893_full_validation.pdf.gz | 702 KB | Display | |
Data in XML | emd_11893_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | emd_11893_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11893 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11893 | HTTPS FTP |
-Related structure data
Related structure data | 7aseMC 7askC 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_11893.map.gz / Format: CCP4 / Size: 244.1 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: 1.1 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 : 43S preinitiation complex from Trypanosoma cruzi with the helicas...
+Supramolecule #1: 43S preinitiation complex from Trypanosoma cruzi with the helicas...
+Macromolecule #1: kDDX60
+Macromolecule #4: 40S ribosomal protein S24
+Macromolecule #5: Elongation initiation factor 2 alpha subunit, putative
+Macromolecule #6: 60S ribosomal protein L40
+Macromolecule #7: Translation initiation factor, putative
+Macromolecule #8: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #9: 40S ribosomal protein S16, putative
+Macromolecule #10: 40S ribosomal protein S18, putative
+Macromolecule #11: 40S ribosomal protein S23, putative
+Macromolecule #12: 40S ribosomal protein S8
+Macromolecule #13: 40S ribosomal protein S5, putative
+Macromolecule #14: 40S ribosomal protein S7
+Macromolecule #15: 40S ribosomal protein S13, putative
+Macromolecule #16: 40S ribosomal protein S27, putative
+Macromolecule #17: 40S ribosomal protein S26
+Macromolecule #18: 40S ribosomal protein S33
+Macromolecule #19: 40S ribosomal protein S14, putative
+Macromolecule #20: 40S ribosomal protein S11, putative
+Macromolecule #21: Putative 40S ribosomal protein S9
+Macromolecule #22: 40S ribosomal protein SA
+Macromolecule #23: 40S ribosomal protein S2, putative
+Macromolecule #24: Putative 40S ribosomal protein S21
+Macromolecule #25: 40S ribosomal protein S25
+Macromolecule #26: RNA-binding protein, putative
+Macromolecule #27: 40S ribosomal protein S12
+Macromolecule #28: Eukaryotic translation initiation factor 2 subunit, putative
+Macromolecule #29: 40S ribosomal protein S6
+Macromolecule #30: 40S ribosomal protein S17, putative
+Macromolecule #31: Ribosomal protein S20, putative
+Macromolecule #32: 40S ribosomal protein S3, putative
+Macromolecule #33: 40S ribosomal protein S10, putative
+Macromolecule #34: Ribosomal protein S19, putative
+Macromolecule #35: 40S ribosomal protein S15a, putative
+Macromolecule #36: 40S ribosomal protein S30
+Macromolecule #37: Protein translation factor SUI1 homolog, putative
+Macromolecule #38: Putative eukaryotic translation initiation factor 1A
+Macromolecule #39: Eukaryotic translation initiation factor 3 subunit E
+Macromolecule #40: Eukaryotic translation initiation factor 5, putative
+Macromolecule #41: Ribosomal protein S29, putative
+Macromolecule #42: eL41
+Macromolecule #43: JAB_MPN domain-containing protein
+Macromolecule #44: CSN8_PSD8_EIF3K domain-containing protein
+Macromolecule #45: 40S ribosomal protein S15, putative
+Macromolecule #46: Eukaryotic translation initiation factor 3 subunit 8, putative
+Macromolecule #47: eIF3A
+Macromolecule #48: 40S ribosomal protein S3a-2
+Macromolecule #49: Eukaryotic translation initiation factor 3 (EIF-3) interacting pr...
+Macromolecule #50: eIF3H
+Macromolecule #51: Eukaryotic translation initiation factor 3 subunit 7-like protein...
+Macromolecule #52: 40S ribosomal protein S4
+Macromolecule #2: initiator tRNA-Met
+Macromolecule #3: 18S
+Macromolecule #53: ZINC ION
+Macromolecule #54: MAGNESIUM ION
+Macromolecule #55: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/2 / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33775 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |