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- EMDB-11895: 43S preinitiation complex from Trypanosoma cruzi with the kDDX60 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-11895
Title43S preinitiation complex from Trypanosoma cruzi with the kDDX60 helicase bound with ATP
Map data
Sample
  • Complex: 43S preinitiation complex from Trypanosoma cruzi with the helicase kDDX60
    • Protein or peptide: kDDX60
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Function / homology
Function and homology information


nucleic acid binding / ATP binding
Similarity search - Function
DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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
ATP-dependent DEAD/H RNA helicase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 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) releaseApr 14, 2021-
Map releaseApr 14, 2021-
UpdateApr 21, 2021-
Current statusApr 21, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0344
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0344
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ask
  • Surface level: 0.0344
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ask
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11895.png

Downloads & links

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Map

FileDownload / File: emd_11895.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.635 Å
Density
Contour LevelBy AUTHOR: 0.0344 / Movie #1: 0.0344
Minimum - Maximum-0.12133194 - 0.2213153
Average (Standard dev.)0.0005708663 (±0.010546387)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 490.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.6351.6351.635
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z490.500490.500490.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.1210.2210.001

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Supplemental data

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Sample components

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Entire : 43S preinitiation complex from Trypanosoma cruzi with the helicas...

EntireName: 43S preinitiation complex from Trypanosoma cruzi with the helicase kDDX60
Components
  • Complex: 43S preinitiation complex from Trypanosoma cruzi with the helicase kDDX60
    • Protein or peptide: kDDX60
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: 43S preinitiation complex from Trypanosoma cruzi with the helicas...

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

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Macromolecule #1: kDDX60

MacromoleculeName: kDDX60 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma cruzi (eukaryote)
Molecular weightTheoretical: 246.749875 KDa
SequenceString: MSSRYRELIA IFGEFLEEND FHVRISMDRV GEVKTLFSAK TIPVESETEA AIEVVTIEAA RRRDALRRTC NAVLRTRHSD QHVDVGTIV ADEEERLAWK FLIGALAAKN SEILPVVEAE LLLAAVEYHY ATARPELCDM FVHLSASEMF FIDGDSLFMA A LSPQSVDW ...String:
MSSRYRELIA IFGEFLEEND FHVRISMDRV GEVKTLFSAK TIPVESETEA AIEVVTIEAA RRRDALRRTC NAVLRTRHSD QHVDVGTIV ADEEERLAWK FLIGALAAKN SEILPVVEAE LLLAAVEYHY ATARPELCDM FVHLSASEMF FIDGDSLFMA A LSPQSVDW DLIQPLHVIY NAQKLLYDMH CRGARFHVVF FDSLLWIWES APAKLFMREN LRKTLMSLSE NDAKVGLSIS NF SSYYSEA FETYVKQWEP EFILMSDGEQ LGRLNPLQAF FVRPSAANNT HDSRRKANYT DADEANPYRL RRQYRSIVED EAV GDKAAL YYRCIHLWAA TRRLKVAYSS RIIYKENAMV VFTVRVDGAS FERAVTIESD VQALAQSMEH EVQLPAISSA SLGL LDEED LSCRERVVYA ALHAYLRASA RSEQEHQLCQ ALAITTYITG YLNKEARAQQ VRPNPILAGF LNEISPFLLA VWRHA DCTN GNGQEFDLID GHLFSAVSQQ LRTASVSELF DEYGVEDIES TWGVLDDQGS ADIVNAPLSY LPVIDSVDVE KLQPYP LIT HELVERLAKG FGISTHRADA PYPTDFGAAN ELAGWDITTP FDRLNDVIDA EGDAIAKSMM TEKEAKNVQE YYKKFVR NA LKQAQSMGIS GFAAHELAMV CSDNDSDDDA GGNSANNKTA GAKKVNKEHA GQRNKKERSK EDEIRERSNV IAATATVA E WHKQMNHLLH AVDMSHGRTT NRDRDESINT IMAAIKRLSQ EKFGKNFDPG YTLGGSTNTA VPLKLEMWRL LVAASQLRE VEFAFAMEDP ALKDSKGASK KKDSKSEYKM LYGFHVINQF VEREAVKGNH WGQLDPLRKA KPDMTIVEAR SYLRWVYLSF VEMHIQLKL KCRVVKLQLE NWRAERERAR LAQESPKIAL GIPLFLYCHH HVLAVIRDEG PRMSSEDIDT VRSALKHFDL P DSYYNKLD QCIARWQNMT LGTLLPSLLP QDKQLFETPE MLQLIHMGHL LERPFVREHD YRVAFNPDNW QRELLDIVDG RG SAVVCAP TSAGKTFISY YCMYKALRRT NKKVVVYLAP ARALINQAVA DVCARYGSKK YKNPGRYIYG ALGGADYHQF HDS CQVLLT VPETFETMLL SPKYTDWVEL IDYVILDEIH SMESNGNGDV WERILALLPC PFVALSATLG ETQQLCSWLN RVQG RLKEQ TEEMSGKMRD FEVHLLPSEG KSIQRWNDIK KYIYLPPPGA ALTQKKIKAQ YNNCYIRDLH PLSILTADQL QRGFP PDIS LVPSEVVSLF EKMHSKFNEV VWPNYSSLQL AKTLRAQLML IEPSKYFEAE TYITQERARQ YEAEVKNAFA YWAYLG HEG CELPENLVEE DLDDFSASMN MAVESILRTF AQKLNEDEAL LERHAADGME KKKRMLLRQQ HLQLLQQQEQ ENEPNQE ES MEQKSEEQGG AQEEEQEKET VGSVSFPGSR QFIREHILNV LRELIARDMG PTIVFSFESE DCGDLVKYVV EQLEEAES R YRKTNEFALY KARIERAAAA QEARRKQRES TLKQKRLTTG DDGDVEVADR DMSDGEGEDE LFVVPDVLPE FTFIGEKCT VEPEVVDSLM EDCEKEGEDL LLRALQRGIG MHHAGVKGKL RAHVERLFRG RHCGVIFSTE TLALGIHSPC RSVVLAGDHI LLNPTQFRQ MMGRAGRRGL DYLGHLVFLG ITMRRIKRLM TSSMTVIKGN VQMDPISNLR LLQLYDFNTL RHLKNEAGWK T HVLKLAER LFVNPLFFQG RNSVAGGNME GFTVEWLQML LGYFQREGLH FSDHASSLGS ILQDAMYVFR EAHVGNEGFS FI RMLTSGV FDKAHYSPLY DKKLNSGVLD EPLAELLAYL FSTHQTCGVP LEMHRSALLD PAVSTLWEGK TGPTQHRAVL SPI DVCSPT IHAFDNTDFF ALLSAFYNYL ASHLAPQTGA ALRLPCMKST NKKCRIFGGG STEFLLKQKL QESSVPYKAR SPFV AISGC GDLFTSVDDV TFTLRDGLYC DRTLLPILDL ADGWRHDGAQ ILINACLLDF LRAKAQIDTT RKNYRFTLLE ELNGL SQSL SYAVLNRAEK ILSNLAGLVR PTKLPRAKVL TAIMPDESEE GIFMAGAPRL LEVAERLNSL QPQIQKRLAE ELLTAK WAK RISEMNAQRK D

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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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 TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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

4f93

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19700

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