6S5Z

Structure of Rib R28N from Streptococcus pyogenes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Defining the remarkable structural malleability of a bacterial surface protein Rib domain implicated in infection.

Whelan, F.Lafita, A.Griffiths, S.C.Cooper, R.E.M.Whittingham, J.L.Turkenburg, J.P.Manfield, I.W.St John, A.N.Paci, E.Bateman, A.Potts, J.R.

(2019) Proc Natl Acad Sci U S A 116: 26540-26548

  • DOI: https://doi.org/10.1073/pnas.1911776116
  • Primary Citation of Related Structures:  
    6S5W, 6S5X, 6S5Y, 6S5Z, 6SX1

  • PubMed Abstract: 

    Streptococcus groups A and B cause serious infections, including early onset sepsis and meningitis in newborns. Rib domain-containing surface proteins are found associated with invasive strains and elicit protective immunity in animal models. Yet, despite their apparent importance in infection, the structure of the Rib domain was previously unknown. Structures of single Rib domains of differing length reveal a rare case of domain atrophy through deletion of 2 core antiparallel strands, resulting in the loss of an entire sheet of the β-sandwich from an immunoglobulin-like fold. Previously, observed variation in the number of Rib domains within these bacterial cell wall-attached proteins has been suggested as a mechanism of immune evasion. Here, the structure of tandem domains, combined with molecular dynamics simulations and small angle X-ray scattering, suggests that variability in Rib domain number would result in differential projection of an N-terminal host-colonization domain from the bacterial surface. The identification of 2 further structures where the typical B-D-E immunoglobulin β-sheet is replaced with an α-helix further confirms the extensive structural malleability of the Rib domain.


  • Organizational Affiliation

    Department of Biology, The University of York, YO10 5DD York, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Surface protein R28
A, B
85Streptococcus pyogenesMutation(s): 0 
Gene Names: spr28
UniProt
Find proteins for Q9XDB6 (Streptococcus pyogenes)
Explore Q9XDB6 
Go to UniProtKB:  Q9XDB6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XDB6
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.423α = 90
b = 43.56β = 118.27
c = 47.615γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
British Heart FoundationUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references
  • Version 1.2: 2022-12-21
    Changes: Database references, Derived calculations