8AXK

Type 3 secretion system export apparatus core, inner rod and needle of Shigella flexneri


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Integrative structural analysis of the type III secretion system needle complex from Shigella flexneri.

Flacht, L.Lunelli, M.Kaszuba, K.Chen, Z.A.Reilly, F.J.O.Rappsilber, J.Kosinski, J.Kolbe, M.

(2023) Protein Sci 32: e4595-e4595

  • DOI: https://doi.org/10.1002/pro.4595
  • Primary Citation of Related Structures:  
    8AXK, 8AXL, 8AXN

  • PubMed Abstract: 

    The type III secretion system (T3SS) is a large, transmembrane protein machinery used by various pathogenic gram-negative bacteria to transport virulence factors into the host cell during infection. Understanding the structure of T3SSs is crucial for future developments of therapeutics that could target this system. However, much of the knowledge about the structure of T3SS is available only for Salmonella, and it is unclear how this large assembly is conserved across species. Here, we combined cryo-electron microscopy, cross-linking mass spectrometry, and integrative modeling to determine the structure of the T3SS needle complex from Shigella flexneri. We show that the Shigella T3SS exhibits unique features distinguishing it from other structurally characterized T3SSs. The secretin pore complex adopts a new fold of its C-terminal S domain and the pilotin MxiM[SctG] locates around the outer surface of the pore. The export apparatus structure exhibits a conserved pseudohelical arrangement but includes the N-terminal domain of the SpaS[SctU] subunit, which was not present in any of the previously published virulence-related T3SS structures. Similar to other T3SSs, however, the apparatus is anchored within the needle complex by a network of flexible linkers that either adjust conformation to connect to equivalent patches on the secretin oligomer or bind distinct surface patches at the same height of the export apparatus. The conserved and unique features delineated by our analysis highlight the necessity to analyze T3SS in a species-specific manner, in order to fully understand the underlying molecular mechanisms of these systems. The structure of the type III secretion system from Shigella flexneri delineates conserved and unique features, which could be used for the development of broad-range therapeutics.


  • Organizational Affiliation

    Department for Structural Infection Biology, Center for Structural Systems Biology (CSSB) & Helmholtz Centre for Infection Research (HZI), Hamburg, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Surface presentation of antigens protein SpaP
A, B, C, D, E
216Shigella flexneriMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A1L3 (Shigella flexneri)
Explore P0A1L3 
Go to UniProtKB:  P0A1L3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A1L3
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Surface presentation of antigens protein SpaR256Shigella flexneriMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A1M6 (Shigella flexneri)
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UniProt GroupP0A1M6
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Surface presentation of antigens protein SpaQ
G, H, I, J
86Shigella flexneriMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A1M4 (Shigella flexneri)
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UniProt GroupP0A1M4
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Surface presentation of antigens protein SpaS342Shigella flexneriMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A1M8 (Shigella flexneri)
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UniProt GroupP0A1M8
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Protein MxiI97Shigella flexneriMutation(s): 0 
UniProt
Find proteins for P0A225 (Shigella flexneri)
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UniProt GroupP0A225
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Protein MxiH98Shigella flexneriMutation(s): 0 
Gene Names: mxiHCP0137
UniProt
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UniProt GroupP0A223
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein MxiD566Shigella flexneriMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q04641 (Shigella flexneri)
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UniProt GroupQ04641
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Lipoprotein MxiJ241Shigella flexneriMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q06081 (Shigella flexneri)
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UniProt GroupQ06081
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.18.2_3874

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2023-03-01 
  • Deposition Author(s): Lunelli, M.

Funding OrganizationLocationGrant Number
Helmholtz AssociationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-01
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references