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- EMDB-11896: 43S preinitiation complex from Leishmania tarentolae with kDDX60 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-11896
Title43S preinitiation complex from Leishmania tarentolae with kDDX60 helicase
Map data
Sample
  • Complex: 43S preinitiation complex from Leishmania tarentolae with the helicase kDDX60
Biological speciesLeishmania tarentolae (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.1 Å
AuthorsBochler A / Brito Querido J / Prilepskaja T / Soufari H / Del Cistia ML / Kuhn L / Rimoldi Ribeiro A / Valasek LS / Hashem Y
Funding support France, Czech Republic, 4 items
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, 2020-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateJun 8, 2022-
Current statusJun 8, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0264
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0264
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11896.png

Downloads & links

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Map

FileDownload / File: emd_11896.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.18 Å
Density
Contour LevelBy AUTHOR: 0.0264 / Movie #1: 0.0264
Minimum - Maximum-0.061527736 - 0.10868906
Average (Standard dev.)-0.00036430827 (±0.0078107603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 471.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.181.181.18
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z472.000472.000472.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0620.109-0.000

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Supplemental data

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Sample components

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Entire : 43S preinitiation complex from Leishmania tarentolae with the hel...

EntireName: 43S preinitiation complex from Leishmania tarentolae with the helicase kDDX60
Components
  • Complex: 43S preinitiation complex from Leishmania tarentolae with the helicase kDDX60

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Supramolecule #1: 43S preinitiation complex from Leishmania tarentolae with the hel...

SupramoleculeName: 43S preinitiation complex from Leishmania tarentolae with the helicase kDDX60
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#52
Source (natural)Organism: Leishmania tarentolae (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5opt

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10144

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