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- PDB-7ask: 43S preinitiation complex from Trypanosoma cruzi with the kDDX60 ... -

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Entry
Database: PDB / ID: 7ask
Title43S preinitiation complex from Trypanosoma cruzi with the kDDX60 helicase bound with ATP
ComponentskDDX60
KeywordsTRANSLATION / preinitiation / factors / kinetoplastid / helicase
Function / homology
Function and homology information


helicase activity / nucleic acid binding / hydrolase activity / ATP binding / cytoplasm
Similarity search - Function
: / : / ATP-dependent RNA helicase DDX60, PIN-like domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily ...: / : / ATP-dependent RNA helicase DDX60, PIN-like domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent DEAD/H RNA helicase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsBochler, 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
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2017-STG#759120TransTryp France
Laboratories of Excellence (LabEx)ANR10LABX0036NETRNA France
Laboratories of Excellence (LabEx)ANR 14 ACHN0024 CryoEM80S France
Czech Science FoundationGrant of Excellence in Basic Research (EXPRO2019) Czech Republic
CitationJournal: 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
DepositionOct 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
F: kDDX60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,2013
Polymers246,7501
Non-polymers4522
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area770 Å2
ΔGint-17 kcal/mol
Surface area85550 Å2
MethodPISA

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Components

#1: Protein kDDX60


Mass: 246749.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4E5Z1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 43S preinitiation complex from Trypanosoma cruzi with the helicase kDDX60
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Trypanosoma cruzi (eukaryote)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19700 / Symmetry type: POINT

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