3V0W

Crystal structure of Fab WN1 222-5 in complex with LPS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Antibody WN1 222-5 mimics Toll-like receptor 4 binding in the recognition of LPS.

Gomery, K.Muller-Loennies, S.Brooks, C.L.Brade, L.Kosma, P.Di Padova, F.Brade, H.Evans, S.V.

(2012) Proc Natl Acad Sci U S A 109: 20877-20882

  • DOI: https://doi.org/10.1073/pnas.1209253109
  • Primary Citation of Related Structures:  
    3V0V, 3V0W

  • PubMed Abstract: 

    Escherichia coli infections, a leading cause of septic shock, remain a major threat to human health because of the fatal action to endotoxin (LPS). Therapeutic attempts to neutralize endotoxin currently focus on inhibiting the interaction of the toxic component lipid A with myeloid differentiating factor 2, which forms a trimeric complex together with Toll-like receptor 4 to induce immune cell activation. The 1.73-Å resolution structure of the unique endotoxin-neutralizing protective antibody WN1 222-5 in complex with the core region shows that it recognizes LPS of all E. coli serovars in a manner similar to Toll-like receptor 4, revealing that protection can be achieved by targeting the inner core of LPS and that recognition of lipid A is not required. Such interference with Toll-like receptor complex formation opens new paths for antibody sepsis therapy independent of lipid A antagonists.


  • Organizational Affiliation

    Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8P 3P6.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
WN1 222-5 Fab (IgG2a) light chainA [auth L]212Mus musculusMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
WN1 222-5 Fab (IgG2a) heavy chainB [auth H]219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-amino-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-[alpha-D-galactopyranose-(1-6)]alpha-D-glucopyranose-(1-3)-[L-glycero-alpha-D-manno-heptopyranose-(1-7)]4-O-phosphono-L-glycero-alpha-D-manno-heptopyranose-(1-3)-4-O-phosphono-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acidC [auth A]10N/A
Glycosylation Resources
GlyTouCan:  G52117HE
GlyCosmos:  G52117HE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.852α = 90
b = 101.852β = 90
c = 118.532γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary