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- PDB-7agx: Apo-state type 3 secretion system export apparatus complex from S... -

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Basic information

Entry
Database: PDB / ID: 7agx
TitleApo-state type 3 secretion system export apparatus complex from Salmonella enterica typhimurium
Components
  • Protein PrgI
  • Protein PrgJ
  • Surface presentation of antigens protein SpaP
  • Surface presentation of antigens protein SpaQ
  • Surface presentation of antigens protein SpaR
KeywordsPROTEIN TRANSPORT / T3SS / Export Apparatus / Injectisome / Needle Complex
Function / homology
Function and homology information


The IPAF inflammasome / type III protein secretion system complex / protein secretion by the type III secretion system / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / protein secretion / protein targeting / protein transport / cell surface / extracellular region ...The IPAF inflammasome / type III protein secretion system complex / protein secretion by the type III secretion system / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / protein secretion / protein targeting / protein transport / cell surface / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
: / Type III secretion protein SpaR/YscT / Type III secretion protein HrpO / Yop virulence translocation protein R / Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / Type III secretion system, needle protein / Bacterial export protein family 3 / Bacterial export proteins, family 3 ...: / Type III secretion protein SpaR/YscT / Type III secretion protein HrpO / Yop virulence translocation protein R / Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / Type III secretion system, needle protein / Bacterial export protein family 3 / Bacterial export proteins, family 3 / Flagella transport protein fliP family signature 1. / Type III secretion system inner membrane P protein / FliP family / Flagella transport protein fliP family signature 2. / Type III secretion system inner membrane R protein / Bacterial export proteins, family 1
Similarity search - Domain/homology
Surface presentation of antigens protein SpaQ / Surface presentation of antigens protein SpaP / Surface presentation of antigens protein SpaR / SPI-1 type 3 secretion system needle filament protein / Protein PrgJ
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGoessweiner-Mohr, N. / Fahrenkamp, D. / Miletic, S. / Wald, J. / Marlovits, T.
Funding support Austria, Germany, 2items
OrganizationGrant numberCountry
Austrian Science FundI 2408-B22 Austria
German Research Foundation (DFG)FA1518/2-1 Germany
CitationJournal: Nat Commun / Year: 2021
Title: Substrate-engaged type III secretion system structures reveal gating mechanism for unfolded protein translocation.
Authors: Sean Miletic / Dirk Fahrenkamp / Nikolaus Goessweiner-Mohr / Jiri Wald / Maurice Pantel / Oliver Vesper / Vadim Kotov / Thomas C Marlovits /
Abstract: Many bacterial pathogens rely on virulent type III secretion systems (T3SSs) or injectisomes to translocate effector proteins in order to establish infection. The central component of the injectisome ...Many bacterial pathogens rely on virulent type III secretion systems (T3SSs) or injectisomes to translocate effector proteins in order to establish infection. The central component of the injectisome is the needle complex which assembles a continuous conduit crossing the bacterial envelope and the host cell membrane to mediate effector protein translocation. However, the molecular principles underlying type III secretion remain elusive. Here, we report a structure of an active Salmonella enterica serovar Typhimurium needle complex engaged with the effector protein SptP in two functional states, revealing the complete 800Å-long secretion conduit and unraveling the critical role of the export apparatus (EA) subcomplex in type III secretion. Unfolded substrates enter the EA through a hydrophilic constriction formed by SpaQ proteins, which enables side chain-independent substrate transport. Above, a methionine gasket formed by SpaP proteins functions as a gate that dilates to accommodate substrates while preventing leaky pore formation. Following gate penetration, a moveable SpaR loop first folds up to then support substrate transport. Together, these findings establish the molecular basis for substrate translocation through T3SSs and improve our understanding of bacterial pathogenicity and motility.
History
DepositionSep 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
1A: Surface presentation of antigens protein SpaP
1B: Surface presentation of antigens protein SpaP
1C: Surface presentation of antigens protein SpaP
1D: Surface presentation of antigens protein SpaP
1E: Surface presentation of antigens protein SpaP
1F: Surface presentation of antigens protein SpaR
1G: Surface presentation of antigens protein SpaQ
1H: Surface presentation of antigens protein SpaQ
1I: Surface presentation of antigens protein SpaQ
1J: Surface presentation of antigens protein SpaQ
1K: Protein PrgJ
1L: Protein PrgJ
1M: Protein PrgJ
1N: Protein PrgJ
1O: Protein PrgJ
1P: Protein PrgJ
2A: Protein PrgI
2B: Protein PrgI
2C: Protein PrgI
2D: Protein PrgI
2E: Protein PrgI
2F: Protein PrgI
2G: Protein PrgI
2H: Protein PrgI
2I: Protein PrgI
2J: Protein PrgI
2K: Protein PrgI
2L: Protein PrgI
2M: Protein PrgI
2N: Protein PrgI
2O: Protein PrgI
2P: Protein PrgI
2Q: Protein PrgI


Theoretical massNumber of molelcules
Total (without water)408,51033
Polymers408,51033
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Surface presentation of antigens protein SpaP


Mass: 25249.596 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P40700
#2: Protein Surface presentation of antigens protein SpaR


Mass: 28499.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P40701
#3: Protein
Surface presentation of antigens protein SpaQ


Mass: 9363.229 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P0A1L7
#4: Protein
Protein PrgJ


Mass: 10934.425 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P41785
#5: Protein
Protein PrgI


Mass: 8864.868 Da / Num. of mol.: 17 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P41784

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Export apparatus core complex with inner rod and needle filament proteins PrgJ and PrgI.
Type: COMPLEX / Details: Apo-state / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.336 MDa / Experimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Cellular location: Membrane
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 31.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: UCSF ChimeraX / Version: 0.93/v8 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package
EM software
IDNameVersionCategory
7Coot0.9bmodel fitting
8ISOLDE1.0b5model fitting
12RELION3classification
14ISOLDE1.0b5model refinement
15PHENIX1.18-6831model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54491 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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