5IO8 | pdb_00005io8

Salmonella Typhimurium VirG-like (STV) protein at 2.19 Angstrom resolution solved by Iodine SAD.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 
    0.245 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5IO8

This is version 1.2 of the entry. See complete history

Literature

Structural investigation on SPI-6-associated Salmonella typhimurium VirG-like stress protein that promotes pathogen survival in macrophages.

Ray, S.Pandey, N.K.Kushwaha, G.S.Das, S.Ganguly, A.K.Vashi, N.Kumar, D.Suar, M.Bhavesh, N.S.

(2022) Protein Sci 31: 835-849

  • DOI: https://doi.org/10.1002/pro.4272
  • Primary Citation Related Structures: 
    5IHF, 5IO8

  • PubMed Abstract: 

    Enteric microbial pathogenesis, remarkably a complex process, is achieved by virulence factors encoded by genes located within regions of the bacterial genome termed pathogenicity islands. Salmonella pathogenicity islands (SPI) encodes proteins, that are essential virulence determinants for pathogen colonization and virulence. In addition to the well-characterized SPI-1 and SPI-2 proteins, which are required for bacterial invasion and intracellular replication, respectively, SPI-6 (formerly known as Salmonella enterica centisome 7 island [SCI]) encoding proteins are also known to play pivotal role in Salmonella pathogenesis. However, the underlying molecular mechanism of these proteins remained elusive. To gain molecular insights into SPI-6-associated proteins, in this study, a SPI-6 Salmonella typhimurium VirG-like protein (STV) is characterized using interdisciplinary experimental approaches including X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy and infection assays. The high-resolution crystal structure, determined by the single-wavelength anomalous dispersion (SAD) method, reveals that STV belongs to the LTxxQ motif family. Solution-state NMR spectroscopy studies reveal that STV form a dimer involving interconnected helices. Interestingly, functional studies show that STV influence pathogen persistence inside macrophages in vitro at later stages of infection. Altogether, our findings suggest that STV, a member of the LTxxQ stress protein family, modulates bacterial survival mechanism in macrophages through SPI-1 and SPI-2 genes, respectively.


  • Organizational Affiliation
    • School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India.

Macromolecule Content 

  • Total Structure Weight: 28.58 kDa 
  • Atom Count: 1,683 
  • Modeled Residue Count: 205 
  • Deposited Residue Count: 232 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
VirG-like protein
A, B
116Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344Mutation(s): 0 
Gene Names: SL1344_RS01575
UniProt
Find proteins for A0A0H3ND95 (Salmonella typhimurium (strain SL1344))
Explore A0A0H3ND95 
Go to UniProtKB:  A0A0H3ND95
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3ND95
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD

Query on IOD



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
PO4

Query on PO4



Download:Ideal Coordinates CCD File
N [auth A],
O [auth A],
P [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA

Query on NA



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A],
L [auth A],
M [auth A],
X [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free:  0.245 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.115α = 90
b = 60.277β = 90
c = 62.603γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
India--

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2026-03-11
    Changes: Database references, Structure summary