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- EMDB-10037: Cryo-EM structure of Yersinia pseudotuberculosis TcaA-TcaB -

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Basic information

Entry
Database: EMDB / ID: EMD-10037
TitleCryo-EM structure of Yersinia pseudotuberculosis TcaA-TcaB
Map dataCryo-EM density map of Yersinia pseudotuberculosis TcaA-TcaB
Sample
  • Complex: Y. pseudotuberculosis TcaA-TcaB pentamer
    • Protein or peptide: 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
Biological speciesYersinia pseudotuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsRoderer D / Leidreiter F / Gatsogiannis C / Meusch D / Benz R / Raunser S
Funding support Germany, 1 items
OrganizationGrant numberCountry
European Research Council615984 Germany
CitationJournal: 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
DepositionJun 4, 2019-
Header (metadata) releaseJul 17, 2019-
Map releaseOct 23, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rwb
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10037.png

Downloads & links

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Map

FileDownload / File: emd_10037.map.gz / Format: CCP4 / Size: 620.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM density map of Yersinia pseudotuberculosis TcaA-TcaB
Voxel sizeX=Y=Z: 0.68 Å
Density
Contour LevelBy AUTHOR: 0.016 / Movie #1: 0.016
Minimum - Maximum-0.03798843 - 0.102317125
Average (Standard dev.)0.00038725912 (±0.0032285964)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions546546546
Spacing546546546
CellA=B=C: 371.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.680.680.68
M x/y/z546546546
origin x/y/z0.0000.0000.000
length x/y/z371.280371.280371.280
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS546546546
D min/max/mean-0.0380.1020.000

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Supplemental data

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Sample components

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Entire : Y. pseudotuberculosis TcaA-TcaB pentamer

EntireName: Y. pseudotuberculosis TcaA-TcaB pentamer
Components
  • Complex: Y. pseudotuberculosis TcaA-TcaB pentamer
    • Protein or peptide: 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

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Supramolecule #1: Y. pseudotuberculosis TcaA-TcaB pentamer

SupramoleculeName: 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
Source (natural)Organism: Yersinia pseudotuberculosis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 1 MDa

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Macromolecule #1: Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative ...

MacromoleculeName: 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
Source (natural)Organism: Yersinia pseudotuberculosis (bacteria)
Molecular weightTheoretical: 231.985031 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: OTHER / Software - Name: SPHIRE
Final angle assignmentType: OTHER / Software - Name: SPHIRE
Final reconstructionApplied 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

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Atomic model buiding 1

Initial modelPDB ID:

1vw1
PDB Unreleased entry

Output model

PDB-6rwb:
Cryo-EM structure of Yersinia pseudotuberculosis TcaA-TcaB

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