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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 109: 20877-20882

  • DOI: 10.1073/pnas.1209253109
  • Primary Citation of Related Structures:  3V0V

  • 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 toxi ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
WN1 222-5 Fab (IgG2a) light chain
L
212N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
WN1 222-5 Fab (IgG2a) heavy chain
H
219N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
H, L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GLC
Query on GLC

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Download CCD File 
H
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
GM0
Query on GM0

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Download CCD File 
H
4-O-phosphono-L-glycero-alpha-D-manno-heptopyranose
C7 H15 O10 P
JDFMKMOMBHLESC-OPTWKVKHSA-N
 Ligand Interaction
PA1
Query on PA1

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Download CCD File 
H
2-amino-2-deoxy-alpha-D-glucopyranose
C6 H13 N O5
MSWZFWKMSRAUBD-UKFBFLRUSA-N
 Ligand Interaction
KDO
Query on KDO

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Download CCD File 
H
3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
C8 H14 O8
NNLZBVFSCVTSLA-HXUQBWEZSA-N
 Ligand Interaction
GLA
Query on GLA

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Download CCD File 
H
ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
 Ligand Interaction
GMH
Query on GMH

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Download CCD File 
H
L-GLYCERO-D-MANNO-HEPTOPYRANOSE
C7 H14 O7
BGWQRWREUZVRGI-QQABCQGCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.182 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 101.852α = 90.00
b = 101.852β = 90.00
c = 118.532γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
MxDCdata collection
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description