4D3E | pdb_00004d3e

Tetramer of IpaD, modified from 2J0O, fitted into negative stain electron microscopy reconstruction of the wild type tip complex from the type III secretion system of Shigella flexneri


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 24.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Three-Dimensional Electron Microscopy Reconstruction and Cysteine-Mediated Crosslinking Provide a Model of the T3Ss Needle Tip Complex.

Cheung, M.Shen, D.Makino, F.Kato, T.Roehrich, A.D.Martinez-Argudo, I.Walker, M.L.Murillo, I.Liu, X.Pain, M.Brown, J.Frazer, G.Mantell, J.Mina, P.Todd, T.Sessions, R.B.Namba, K.Blocker, A.J.

(2015) Mol Microbiol 95: 31

  • DOI: https://doi.org/10.1111/mmi.12843
  • Primary Citation Related Structures: 
    4D3E

  • PubMed Abstract: 

    Type III secretion systems are found in many Gram-negative bacteria. They are activated by contact with eukaryotic cells and inject virulence proteins inside them. Host cell detection requires a protein complex located at the tip of the device's external injection needle. The Shigella tip complex (TC) is composed of IpaD, a hydrophilic protein, and IpaB, a hydrophobic protein, which later forms part of the injection pore in the host membrane. Here we used labelling and crosslinking methods to show that TCs from a ΔipaB strain contain five IpaD subunits while the TCs from wild-type can also contain one IpaB and four IpaD subunits. Electron microscopy followed by single particle and helical image analysis was used to reconstruct three-dimensional images of TCs at ∼ 20 Å resolution. Docking of an IpaD crystal structure, constrained by the crosslinks observed, reveals that TC organisation is different from that of all previously proposed models. Our findings suggest new mechanisms for TC assembly and function. The TC is the only site within these secretion systems targeted by disease-protecting antibodies. By suggesting how these act, our work will allow improvement of prophylactic and therapeutic strategies.


  • Organizational Affiliation
    • Schools of Cellular & Molecular Medicine and Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.

Macromolecule Content 

  • Total Structure Weight: 23.08 kDa 
  • Atom Count: 1,621 
  • Modeled Residue Count: 208 
  • Deposited Residue Count: 208 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
INVASIN IPADA [auth D]208Shigella flexneri 5a str. M90TMutation(s): 0 
UniProt
Find proteins for P18013 (Shigella flexneri)
Explore P18013 
Go to UniProtKB:  P18013
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18013
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 24.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN2
RECONSTRUCTIONSPIDER

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Data collection
  • Version 1.3: 2018-01-31
    Changes: Data processing
  • Version 1.4: 2020-04-29
    Changes: Data processing
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references, Refinement description