6SX1

Structure of Rib Standard, a Rib domain from Lactobacillus acidophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å

wwPDB Validation 3D Report Full Report


This is version 1.0 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.USA --: --

  • DOI: 10.1073/pnas.1911776116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • <i>Streptococcus </i> 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 ...

    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; agb@ebi.ac.uk jennifer.potts@york.ac.uk.,European Molecular Biology Laboratory, European Bioinformatics Institute, CB10 1SD Hinxton, United Kingdom.,Department of Biology, The University of York, YO10 5DD York, United Kingdom.,Astbury Centre for Structural Molecular Biology, The University of Leeds, LS2 9JT Leeds, United Kingdom.,European Molecular Biology Laboratory, European Bioinformatics Institute, CB10 1SD Hinxton, United Kingdom; agb@ebi.ac.uk jennifer.potts@york.ac.uk.,York Structural Biology Laboratory, Department of Chemistry, The University of York, YO10 5DD York, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Surface protein
A
83Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM)Mutation(s): 0 
Find proteins for Q5FIM8 (Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM))
Go to UniProtKB:  Q5FIM8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 30.183α = 90.00
b = 32.644β = 90.00
c = 62.811γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
xia2data reduction
Aimlessdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited Kingdom--
British Heart FoundationUnited Kingdom--

Revision History 

  • Version 1.0: 2019-12-18
    Type: Initial release