7ASE | pdb_00007ase

43S preinitiation complex from Trypanosoma cruzi with the kDDX60 helicase

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.33 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural Differences in Translation Initiation between Pathogenic Trypanosomatids and Their Mammalian Hosts.

Bochler, A., Querido, J.B., Prilepskaja, T., Soufari, H., Simonetti, A., Del Cistia, M.L., Kuhn, L., Ribeiro, A.R., Valasek, L.S., Hashem, Y.

(2020) Cell Rep 33: 108534-108534

  • DOI: https://doi.org/10.1016/j.celrep.2020.108534
  • Primary Citation of Related Structures:  
    7ASE, 7ASK

  • PubMed 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 i Met 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 S , 7 S , and 6 S , 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.

    • Organizational Affiliation: 
    • INSERM U1212 (ARNA), Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
kDDX60A [auth f]2,174Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4E5Z1 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24D [auth y]137Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4DW38 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation initiation factor 2 alpha subunit, putativeE [auth s]418Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4E620 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L40F [auth j]150Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for A0A2V2VP49 (Trypanosoma cruzi)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor, putativeG [auth n]343Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4DH88 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinH [auth p]318Trypanosoma cruziMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16, putativeI [auth r]149Trypanosoma cruziMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18, putativeJ [auth u]153Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4E093 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23, putativeK [auth m]143Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4DTQ1 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8L [auth Z]221Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4DU83 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5, putativeM [auth o]190Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4E0Q3 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7N [auth q]211Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4CUC7 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13, putativeO [auth R]151Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4DC38 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27, putativeP [auth S]86Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4DN73 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26Q [auth t]112Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4CYE4 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S33R [auth U]91Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for A0A061J677 (Trypanosoma rangeli SC58)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14, putativeS [auth v]144Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4D6I5 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11, putativeT [auth X]173Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4D0U7 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S9U [auth B]190Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for A0A2V2WBN2 (Trypanosoma cruzi)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAV [auth F]245Trypanosoma cruziMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2, putativeW [auth d]263Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4DIZ9 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S21X [auth g]247Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for A0A2V2UKQ3 (Trypanosoma cruzi)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25Y [auth a]110Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4DTX6 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein, putativeZ [auth J]257Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4DY32 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12AA [auth h]141Trypanosoma cruziMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit, putativeBA [auth 5]477Trypanosoma cruziMutation(s): 0 
EC: 3.6.5.3
UniProt
Find proteins for Q4CPV7 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6CA [auth P]250Trypanosoma cruziMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17, putativeDA [auth i]141Trypanosoma cruziMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S20, putativeEA [auth L]117Trypanosoma cruziMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3, putativeFA [auth M]214Trypanosoma cruziMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10, putativeGA [auth N]161Trypanosoma cruziMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S19, putativeHA [auth O]167Trypanosoma cruziMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15a, putativeIA [auth b]145Trypanosoma cruziMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30JA [auth c]66Trypanosoma cruziMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Protein translation factor SUI1 homolog, putativeKA [auth V]109Trypanosoma cruziMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Putative eukaryotic translation initiation factor 1ALA [auth w]166Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for A0A2V2WGW5 (Trypanosoma cruzi)
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit EMA [auth E]407Trypanosoma cruziMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 5, putativeNA [auth Y]379Trypanosoma cruziMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S29, putativeOA [auth Q]57Trypanosoma cruziMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
eL41PA [auth D]34Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for G0U1J3 (Trypanosoma vivax (strain Y486))
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
JAB_MPN domain-containing proteinQA [auth G]345Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4DQZ2 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
CSN8_PSD8_EIF3K domain-containing proteinRA [auth K]203Trypanosoma cruziMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15, putativeSA [auth T]152Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4DGZ5 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit 8, putativeTA [auth C]716Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4E3G1 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
eIF3AUA [auth 8]762Trypanosoma cruziMutation(s): 0 
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Find proteins for Q4DL69 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3a-2VA [auth W]254Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for Q4DZ41 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 (EIF-3) interacting protein, putativeWA [auth I]489Trypanosoma cruziMutation(s): 0 
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Find proteins for Q4D5W3 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
eIF3HXA [auth H]334Trypanosoma cruziMutation(s): 0 
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Find proteins for Q4DSJ1 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit 7-like protein, putativeYA [auth A]502Trypanosoma cruziMutation(s): 0 
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Find proteins for Q4DCN0 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4ZA [auth l]273Trypanosoma cruziMutation(s): 0 
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Find proteins for O62594 (Trypanosoma cruzi)
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Entity ID: 2
MoleculeChains LengthOrganismImage
initiator tRNA-MetB [auth 1]75Trypanosoma cruzi
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Entity ID: 3
MoleculeChains LengthOrganismImage
18SC [auth 0]2,319Trypanosoma cruzi
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.33 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research Council (ERC)FranceERC-2017-STG#759120TransTryp
Laboratories of Excellence (LabEx)FranceANR10LABX0036NETRNA
Laboratories of Excellence (LabEx)FranceANR 14 ACHN0024 CryoEM80S
Czech Science FoundationCzech RepublicGrant of Excellence in Basic Research (EXPRO2019)

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2021-04-21
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Structure summary