7WVH | pdb_00007wvh

Structure of NAD+ glycohydrolase/Streptolysin O complex from Group A streptococcus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.265 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis underlying the synergism of NADase and SLO during group A Streptococcus infection.

Tsai, W.J.Lai, Y.H.Shi, Y.A.Hammel, M.Duff, A.P.Whitten, A.E.Wilde, K.L.Wu, C.M.Knott, R.Jeng, U.S.Kang, C.Y.Hsu, C.Y.Wu, J.L.Tsai, P.J.Chiang-Ni, C.Wu, J.J.Lin, Y.S.Liu, C.C.Senda, T.Wang, S.

(2023) Commun Biol 6: 124-124

  • DOI: https://doi.org/10.1038/s42003-023-04502-0
  • Primary Citation of Related Structures:  
    7WVH

  • PubMed Abstract: 

    Group A Streptococcus (GAS) is a strict human pathogen possessing a unique pathogenic trait that utilizes the cooperative activity of NAD + -glycohydrolase (NADase) and Streptolysin O (SLO) to enhance its virulence. How NADase interacts with SLO to synergistically promote GAS cytotoxicity and intracellular survival is a long-standing question. Here, the structure and dynamic nature of the NADase/SLO complex are elucidated by X-ray crystallography and small-angle scattering, illustrating atomic details of the complex interface and functionally relevant conformations. Structure-guided studies reveal a salt-bridge interaction between NADase and SLO is important to cytotoxicity and resistance to phagocytic killing during GAS infection. Furthermore, the biological significance of the NADase/SLO complex in GAS virulence is demonstrated in a murine infection model. Overall, this work delivers the structure-functional relationship of the NADase/SLO complex and pinpoints the key interacting residues that are central to the coordinated actions of NADase and SLO in the pathogenesis of GAS infection.


  • Organizational Affiliation

    Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD+-glycohydrolaseA,
D [auth B]
268Streptococcus pyogenes A20Mutation(s): 2 
Gene Names: spn
UniProt
Find proteins for Q9RF14 (Streptococcus pyogenes)
Explore Q9RF14 
Go to UniProtKB:  Q9RF14
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RF14
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Streptolysin OB [auth D],
C
472Streptococcus pyogenes A20Mutation(s): 0 
Gene Names: sloSPy_0167M5005_Spy0141
UniProt
Find proteins for P0C0I3 (Streptococcus pyogenes serotype M1)
Explore P0C0I3 
Go to UniProtKB:  P0C0I3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0I3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 246.094α = 90
b = 52.477β = 132.04
c = 169.397γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)TaiwanMOST 109-2320-B-006-066

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description