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Yorodumi- EMDB-11895: 43S preinitiation complex from Trypanosoma cruzi with the kDDX60 ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11895 | |||||||||||||||
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Title | 43S preinitiation complex from Trypanosoma cruzi with the kDDX60 helicase bound with ATP | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | preinitiation / factors / kinetoplastid / helicase / TRANSLATION | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Trypanosoma cruzi (eukaryote) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 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_11895.map.gz | 95.2 MB | EMDB map data format | |
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Header (meta data) | emd-11895-v30.xml emd-11895.xml | 12.9 KB 12.9 KB | Display Display | EMDB header |
Images | emd_11895.png | 78 KB | ||
Filedesc metadata | emd-11895.cif.gz | 6.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11895 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11895 | HTTPS FTP |
-Validation report
Summary document | emd_11895_validation.pdf.gz | 673.4 KB | Display | EMDB validaton report |
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Full document | emd_11895_full_validation.pdf.gz | 672.9 KB | Display | |
Data in XML | emd_11895_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_11895_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11895 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11895 | HTTPS FTP |
-Related structure data
Related structure data | 7askMC 7aseC C: citing same article (ref.) M: atomic model generated by this map |
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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_11895.map.gz / Format: CCP4 / Size: 103 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: 1.635 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...
Entire | Name: 43S preinitiation complex from Trypanosoma cruzi with the helicase kDDX60 |
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Components |
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-Supramolecule #1: 43S preinitiation complex from Trypanosoma cruzi with the helicas...
Supramolecule | Name: 43S preinitiation complex from Trypanosoma cruzi with the helicase kDDX60 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Trypanosoma cruzi (eukaryote) |
-Macromolecule #1: kDDX60
Macromolecule | Name: kDDX60 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Trypanosoma cruzi (eukaryote) |
Molecular weight | Theoretical: 246.749875 KDa |
Sequence | String: 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 UniProtKB: ATP-dependent DEAD/H RNA helicase |
-Macromolecule #2: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-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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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: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19700 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |