3V0V

Fab WN1 222-5 unliganded


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.5 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
WN1 222-5 Fab (IgG2a) light chainA [auth L],
C [auth B]
212Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
WN1 222-5 Fab (IgG2a) heavy chainB [auth H],
D [auth A]
220Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.886α = 90
b = 48.201β = 110.55
c = 140.131γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CrystalCleardata reduction
d*TREKdata scaling
PHASERphasing
d*TREKdata reduction

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: 2018-03-07
    Changes: Data collection
  • Version 1.3: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-10-16
    Changes: Structure summary