9MLP | pdb_00009mlp

Crystal structure of VgrS from Salmonella Typhimurium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.252 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the type VI secretion protein VgrS from Salmonella Typhimurium.

Sachar, K.Van Schepdael, M.Winters, K.L.Prehna, G.

(2026) J Struct Biol 218: 108297-108297

  • DOI: https://doi.org/10.1016/j.jsb.2026.108297
  • Primary Citation of Related Structures:  
    9MLP

  • PubMed Abstract: 

    Enteric bacterial pathogens employ various strategies to colonize the intestine and cause diseases ranging from gastroenteritis to systemic infections. For example, Salmonella enterica utilizes a nanomachine known as the type VI secretion system (T6SS) to facilitate colonization of the host gut. However, the varied mechanistic details of how the T6SS is loaded with effector proteins remains to be elucidated. Here, we present an X-ray crystal structure of the Salmonella Typhimurium VgrG (VgrS) that serves as platform for T6SS effector loading. Compared to other known structures of VgrG proteins, the VgrS trimer adopts an alternative open conformation within the gp27 region base. The open conformation is due to an extended loop conformation in the gp27 region. This conformation creates a domain extension which docks into the neighboring monomer sequentially around the trimer. Additionally, a comparative structural analysis of VgrS with other VgrG proteins reveals molecular variations that may contribute to specific effector loading mechanisms. Our structural data and molecular analysis highlight the observation that the T6SS of each bacterial species or strain is unique.


  • Organizational Affiliation
    • Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytoplasmic protein
A, B, C
674Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 0 
Gene Names: STM0289
UniProt
Find proteins for Q8ZRL1 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q8ZRL1 
Go to UniProtKB:  Q8ZRL1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZRL1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
U [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
P [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.252 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.147α = 90
b = 209.917β = 90
c = 470.971γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaP.J.T-180450

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-28
    Type: Initial release
  • Version 1.1: 2026-02-11
    Changes: Database references, Structure summary
  • Version 1.2: 2026-03-04
    Changes: Database references
  • Version 1.3: 2026-03-11
    Changes: Database references