6XRB

Crystal structure of SciW from Salmonella typhimurium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis for effector transmembrane domain recognition by type VI secretion system chaperones.

Ahmad, S.Tsang, K.K.Sachar, K.Quentin, D.Tashin, T.M.Bullen, N.P.Raunser, S.McArthur, A.G.Prehna, G.Whitney, J.C.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.62816
  • Primary Citation of Related Structures:  
    6XRB, 6XRF, 6XRR

  • PubMed Abstract: 

    Type VI secretion systems (T6SSs) deliver antibacterial effector proteins between neighboring bacteria. Many effectors harbor N-terminal t rans m embrane d omains (TMDs) implicated in effector translocation across target cell membranes. However, the distribution of these TMD-containing effectors remains unknown. Here, we discover prePAAR, a conserved motif found in over 6000 putative TMD-containing effectors encoded predominantly by 15 genera of Proteobacteria. Based on differing numbers of TMDs, effectors group into two distinct classes that both require a member of the Eag family of T6SS chaperones for export. Co-crystal structures of class I and class II effector TMD-chaperone complexes from Salmonella Typhimurium and Pseudomonas aeruginosa , respectively, reveals that Eag chaperones mimic transmembrane helical packing to stabilize effector TMDs. In addition to participating in the chaperone-TMD interface, we find that prePAAR residues mediate effector-VgrG spike interactions. Taken together, our findings reveal mechanisms of chaperone-mediated stabilization and secretion of two distinct families of T6SS membrane protein effectors.


  • Organizational Affiliation

    Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SciW153Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344Mutation(s): 0 
Gene Names: sciWSL1344_0285
UniProt
Find proteins for A0A0H3NHS6 (Salmonella typhimurium (strain SL1344))
Explore A0A0H3NHS6 
Go to UniProtKB:  A0A0H3NHS6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3NHS6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SciW153Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344Mutation(s): 0 
Gene Names: sciWSL1344_0285
UniProt
Find proteins for A0A0H3NHS6 (Salmonella typhimurium (strain SL1344))
Explore A0A0H3NHS6 
Go to UniProtKB:  A0A0H3NHS6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3NHS6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
C [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CME
Query on CME
B
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.269α = 90
b = 75.093β = 90
c = 76.599γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
Cootmodel building
PHENIXmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2018-04968

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release