6POO

Novel structure of the N-terminal helical domain of BibA, a group B streptococcus immunogenic bacterial adhesin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Novel structure of the N-terminal helical domain of BibA, a group B streptococcus immunogenic bacterial adhesin.

Manne, K.Chattopadhyay, D.Agarwal, V.Blom, A.M.Khare, B.Chakravarthy, S.Chang, C.Ton-That, H.Narayana, S.V.L.

(2020) Acta Crystallogr D Struct Biol 76: 759-770

  • DOI: https://doi.org/10.1107/S2059798320008116
  • Primary Citation of Related Structures:  
    6POO

  • PubMed Abstract: 

    BibA, a group B streptococcus (GBS) surface protein, has been shown to protect the pathogen from phagocytic killing by sequestering a complement inhibitor: C4b-binding protein (C4BP). Here, the X-ray crystallographic structure of a GBS BibA fragment (BibA 126-398 ) and a low-resolution small-angle X-ray scattering (SAXS) structure of the full-length N-terminal domain (BibA 34-400 ) are described. The BibA 126-398 fragment crystal structure displayed a novel and predominantly helical structure. The tertiary arrangement of helices forms four antiparallel three-helix-bundle-motif repeats, with one long helix from a bundle extending into the next. Multiple mutations on recombinant BibA 34-400 delayed the degradation of the protein, and circular dichroism spectroscopy of BibA 34-400 suggested a similar secondary-structure composition to that observed in the crystallized BibA 126-398 fragment. A model was generated for the 92 N-terminal residues (BibA 34-125 ) using structural similarity prediction programs, and a BibA 34-400 model was generated by combining the coordinates of BibA 34-126 and BibA 126-398 . The X-ray structure of BibA 126-398 and the model of BibA 34-400 fitted well into the calculated SAXS envelope. One possible binding site for the BibA N-terminal domain was localized to the N-terminal CCP (complement-control protein) domains of the C4BP α-chain, as indicated by the decreased binding of BibA to a ΔCCP1 C4BP α-chain mutant. In summary, it is suggested that the GBS surface protein BibA, which consists of three antiparallel α-helical-bundle motifs, is unique and belongs to a new class of Gram-positive surface adhesins.


  • Organizational Affiliation

    Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birningham, AL 35294, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BibA273Streptococcus agalactiaeMutation(s): 0 
Gene Names: gbs2018
UniProt
Find proteins for Q8DWZ6 (Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R))
Explore Q8DWZ6 
Go to UniProtKB:  Q8DWZ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DWZ6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.419α = 90
b = 68.814β = 90
c = 199.377γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
CRANK2phasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release