8S5T | pdb_00008s5t

Structure of SemD in complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.237 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Chlamydia pneumoniae effector SemD exploits its host's endocytic machinery by structural and functional mimicry.

Kocher, F.Applegate, V.Reiners, J.Port, A.Spona, D.Hansch, S.Mirzaiebadizi, A.Ahmadian, M.R.Smits, S.H.J.Hegemann, J.H.Molleken, K.

(2024) Nat Commun 15: 7294-7294

  • DOI: https://doi.org/10.1038/s41467-024-51681-3
  • Primary Citation of Related Structures:  
    8S5R, 8S5T

  • PubMed Abstract: 

    To enter epithelial cells, the obligate intracellular pathogen Chlamydia pneumoniae secretes early effector proteins, which bind to and modulate the host-cell's plasma membrane and recruit several pivotal endocytic host proteins. Here, we present the high-resolution structure of an entry-related chlamydial effector protein, SemD. Co-crystallisation of SemD with its host binding partners demonstrates that SemD co-opts the Cdc42 binding site to activate the actin cytoskeleton regulator N-WASP, making active, GTP-bound Cdc42 superfluous. While SemD binds N-WASP much more strongly than Cdc42 does, it does not bind the Cdc42 effector protein FMNL2, indicating effector protein specificity. Furthermore, by identifying flexible and structured domains, we show that SemD can simultaneously interact with the membrane, the endocytic protein SNX9, and N-WASP. Here, we show at the structural level how a single effector protein can hijack central components of the host's endocytic system for efficient internalization.


  • Organizational Affiliation
    • Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Functional Microbial Genomics, Düsseldorf, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Effector SemDA [auth D]326ChlamydiaMutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q9Z7M7 (Chlamydia pneumoniae)
Explore Q9Z7M7 
Go to UniProtKB:  Q9Z7M7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Z7M7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Neural Wiskott-Aldrich syndrome proteinB [auth A]93Rattus norvegicusMutation(s): 0 
Gene Names: WASL
UniProt
Find proteins for O08816 (Rattus norvegicus)
Explore O08816 
Go to UniProtKB:  O08816
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO08816
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.222α = 90
b = 120.222β = 90
c = 65.241γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany417919780
German Research Foundation (DFG)Germany267205415

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-07
    Type: Initial release
  • Version 1.1: 2025-02-19
    Changes: Database references, Structure summary