5M63

Crystal structure of group B Streptococcus type III DP2 oligosaccharide bound to Fab NVS-1-19-5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a protective epitope of group B Streptococcus type III capsular polysaccharide.

Carboni, F.Adamo, R.Fabbrini, M.De Ricco, R.Cattaneo, V.Brogioni, B.Veggi, D.Pinto, V.Passalacqua, I.Oldrini, D.Rappuoli, R.Malito, E.Margarit, I.Y.R.Berti, F.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 5017-5022

  • DOI: 10.1073/pnas.1701885114

  • PubMed Abstract: 
  • Despite substantial progress in the prevention of group B Streptococcus (GBS) disease with the introduction of intrapartum antibiotic prophylaxis, this pathogen remains a leading cause of neonatal infection. Capsular polysaccharide conjugate vaccines ...

    Despite substantial progress in the prevention of group B Streptococcus (GBS) disease with the introduction of intrapartum antibiotic prophylaxis, this pathogen remains a leading cause of neonatal infection. Capsular polysaccharide conjugate vaccines have been tested in phase I/II clinical studies, showing promise for further development. Mapping of epitopes recognized by protective antibodies is crucial for understanding the mechanism of action of vaccines and for enabling antigen design. In this study, we report the structure of the epitope recognized by a monoclonal antibody with opsonophagocytic activity and representative of the protective response against type III GBS polysaccharide. The structure and the atomic-level interactions were determined by saturation transfer difference (STD)-NMR and X-ray crystallography using oligosaccharides obtained by synthetic and depolymerization procedures. The GBS PSIII epitope is made by six sugars. Four of them derive from two adjacent repeating units of the PSIII backbone and two of them from the branched galactose-sialic acid disaccharide contained in this sequence. The sialic acid residue establishes direct binding interactions with the functional antibody. The crystal structure provides insight into the molecular basis of antibody-carbohydrate interactions and confirms that the conformational epitope is not required for antigen recognition. Understanding the structural basis of immune recognition of capsular polysaccharide epitopes can aid in the design of novel glycoconjugate vaccines.


    Organizational Affiliation

    GSK Vaccines, 53100 Siena, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H chain of Fab NVS-1-19-5
H, M
248N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
L chain of Fab NVS-1-19-5
L, N
239N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

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Download CCD File 
L, N
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
GAL
Query on GAL

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Download CCD File 
H, L, M, N
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
H, L, M, N
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
7GW
Query on 7GW

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Download CCD File 
H, M
(2~{R},3~{R},4~{S},5~{S})-2-[bis(oxidanyl)methyl]-5-(hydroxymethyl)oxolane-3,4-diol
C6 H12 O6
IRLQCNDEPRBYOU-NRXMZTRTSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
L, N
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SIA
Query on SIA

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Download CCD File 
H, L, M, N
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.236 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 135.341α = 90.00
b = 142.231β = 90.00
c = 144.732γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-05-17
    Type: Database references
  • Version 1.2: 2017-08-16
    Type: Data collection
  • Version 1.3: 2019-04-03
    Type: Data collection, Source and taxonomy