+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10037 | |||||||||
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Title | Cryo-EM structure of Yersinia pseudotuberculosis TcaA-TcaB | |||||||||
Map data | Cryo-EM density map of Yersinia pseudotuberculosis TcaA-TcaB | |||||||||
Sample |
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Keywords | Toxin / membrane permeation / translocation / complex | |||||||||
Biological species | Yersinia pseudotuberculosis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.25 Å | |||||||||
Authors | Roderer D / Leidreiter F | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Sci Adv / Year: 2019 Title: Common architecture of Tc toxins from human and insect pathogenic bacteria. Authors: F Leidreiter / D Roderer / D Meusch / C Gatsogiannis / R Benz / S Raunser / Abstract: Tc toxins use a syringe-like mechanism to penetrate the membrane and translocate toxic enzymes into the host cytosol. They are composed of three components: TcA, TcB, and TcC. Low-resolution ...Tc toxins use a syringe-like mechanism to penetrate the membrane and translocate toxic enzymes into the host cytosol. They are composed of three components: TcA, TcB, and TcC. Low-resolution structures of TcAs from different bacteria suggest a considerable difference in their architecture and possibly in their mechanism of action. Here, we present high-resolution structures of five TcAs from insect and human pathogens, which show a similar overall composition and domain organization. Essential structural features, including a trefoil protein knot, are present in all TcAs, suggesting a common mechanism of action. All TcAs form functional pores and can be combined with TcB-TcC subunits from other species to form active chimeric holotoxins. We identified a conserved ionic pair that stabilizes the shell, likely operating as a strong latch that only springs open after destabilization of other regions. Our results provide new insights into the architecture and mechanism of the Tc toxin family. | |||||||||
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_10037.map.gz | 47.9 MB | EMDB map data format | |
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Header (meta data) | emd-10037-v30.xml emd-10037.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
Images | emd_10037.png | 71.1 KB | ||
Filedesc metadata | emd-10037.cif.gz | 6.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10037 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10037 | HTTPS FTP |
-Validation report
Summary document | emd_10037_validation.pdf.gz | 242.8 KB | Display | EMDB validaton report |
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Full document | emd_10037_full_validation.pdf.gz | 241.9 KB | Display | |
Data in XML | emd_10037_validation.xml.gz | 8.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10037 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10037 | HTTPS FTP |
-Related structure data
Related structure data | 6rwbMC 6rw6C 6rw8C 6rw9C 6rwaC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10037.map.gz / Format: CCP4 / Size: 620.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM density map of Yersinia pseudotuberculosis TcaA-TcaB | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.68 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 : Y. pseudotuberculosis TcaA-TcaB pentamer
Entire | Name: Y. pseudotuberculosis TcaA-TcaB pentamer |
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Components |
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-Supramolecule #1: Y. pseudotuberculosis TcaA-TcaB pentamer
Supramolecule | Name: Y. pseudotuberculosis TcaA-TcaB pentamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Each protomer is a fusion protein of TcaA and TcaB |
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Source (natural) | Organism: Yersinia pseudotuberculosis (bacteria) |
Molecular weight | Theoretical: 1 MDa |
-Macromolecule #1: Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative ...
Macromolecule | Name: Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit ...Name: Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Yersinia pseudotuberculosis (bacteria) |
Molecular weight | Theoretical: 231.985031 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MASQDNIDHT ASVIADTDNT IHQQAKAEER HRQAARRATQ LRNDPVLSGI NKLAFSVAPK ILQPEARTDL SLAEGIPERA NEYADPASI QSLFSPGRYL CELYHVAKEL HEDGNKLHID KRRPDLQDLV LNNSNMNQEV SSLEILLNVL QTKTPLDELT K DTEAHAND ...String: MASQDNIDHT ASVIADTDNT IHQQAKAEER HRQAARRATQ LRNDPVLSGI NKLAFSVAPK ILQPEARTDL SLAEGIPERA NEYADPASI QSLFSPGRYL CELYHVAKEL HEDGNKLHID KRRPDLQDLV LNNSNMNQEV SSLEILLNVL QTKTPLDELT K DTEAHAND SSFTLPYDDN LTVINAILED KAISLREIAV LLTEESDFSP TPALVQEQLG LNPASYALID IKSPLDESYA KR LAHATQL SVEQLQWLNK NAIENSSNKN DPAKLEILAV ISEYRRLHQR YGLSVDPFIA IINAVNTTHT NENKTSFFQQ IFS TLDVDA GFNFLDQGSW EVIIRKALGI TAEELLRIAK YCFGKSSISN VKMNSKKFSQ LYRMAMIPRT LGVSFSQAEY LWQL YSHSD ENIMEKIAQG NALTIIDAII VLENTLQWMS EQKLDITTLQ AMLTKQYSTT ATPELFNFLS NIYQTLGKQV YSESL KPNL YRSLANGFHL KANVVAGLVN WLAKNDSEFT LERFWQNISM TFAEEPSLHQ LEVHQPLLIQ CQKLSQYVLI AQWAEL SEQ EIALILLPNG IDNRGSAPSP SITLLKLLSE FKLCQQEAKV SQSELFDIMQ QLITDTNEKQ EKLRNSADKV IRSIAKS IG SINNSMDDID STISIRNGSA TLFPPEHPMY KALKLEVSNL EKSKIQLEGK KKEEEIKLEQ AKDNIQSLIN NWDSEIII R LADAYHWDIN IANSMFILIF GEKINFTFHY ENRNDYHYEE HYGYRFEQKP MYSFDKKLTN GFGSILLLKN HIYIAEKLK IHPGTIIKIK NYIFDDKSNE LENIANKLRV NLGSPTSTVL NKINESRRDA LVNYYLAKNV SGDEKIKTAE QLYQYLLLDT KIGHEVKTS PIAEAISSLQ IYINRCVDGE ENDLHEKNIS THFSSDNFLH GWNSYNKRYA RWAGKEKLMY YAADYIDPTL R YNKTELFN TFEQSINNSR LTEKSVKSAL QSYLISYEKL AQIDTIKELY VENIKTHFFL GKTRESPCQY YWRSGEQLSN DS HHLRWSE WKKVECNING TEEKFFINLS WYRNRLYVDW LNKTAFKTDE GKGKSEYHYN AAYKNDNNAW NDNISNMKIG LPW EQSKDI DEIPPIFINQ DNVNSNSKNE TYFITSGSTI NNIPLFHGGY LEGEIKISFD KNKVKFTLEK PFERINEKSD YVIQ INADM SDFNEIKNEK GESVTVEIKK NFNIMAYSLD EEYLGGNSFN RITFDTNIIH ELDGDISLLP PDSLPLVEKL QTSVD ELLS YSTQKDKIGL DAFSGSYGIY FWEFFFHIPF LASMRFLNEQ RFDLAQHWLK YLLNSAGYRD RNGNLLKEGD NILYWN SLP LQQDTDWDKN TLTLPTDDPD VIAMQDPMQY KLAIFMRTLD LIISQGDQAY RQLERDTLAE AKIYYIQASQ LLGSRPD LN RGHQWENIKL AEESRQAENG HFLPPYNEIL LSYWDKLEIR LYNLRHNLNL DGQPLHLPLF ATPVDPKALQ RQHGAGNG I NSGEQMATAQ TSLYRFPLLI ERAKSAVSSV IQFGNSLQSV LERQDNEAMT LLFQQQQQKV LQHTKDIQNN NIQVLQANL EATNSLKSAA KQRSKHYKEL LDNGISSREQ SGLDLRIDAG AVNIASVAPL MLAAALDTAP NVFGLADGGS HWGAVPYATS ATLQISAGL TESRANINDI KANYDRREQE WTLQKNQADK DAEQLAHQYT SVQEQLNMAQ KQRNLAELEQ GHADALYQMQ S TRFTGKEL YNWMAGRLSG LYFQLFDATQ PLCLMAKAVL EKEVDKAKTD GLFIRSGWND LYQGLLAGED LQLNLQKLEN VW LMEEQRA LEVERTVSLA QHYQQLSDHK FNLAEIVTGY MAQDKDQKTG NEQDFVELKN STLIASLSIK GLNLVEDYPE TMH LGDIRR IKQISVSLPA LLGPYQDVQA TLDYAGENTH LAKGCTALAI SRGMNDSGQF QLDFNDGKYL PFEGIDISDK GTLV LRFPN ATSKQKLLLQ SLSDIILHIR YTIRS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.5 sec. / Average electron dose: 130.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Applied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Number images used: 237295 |
Initial angle assignment | Type: OTHER / Software - Name: SPHIRE |
Final angle assignment | Type: OTHER / Software - Name: SPHIRE |