4ODT

Fab Structure of lipid A-specific antibody S1-15 in complex with lipid A carbohydrate backbone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis for Antibody Recognition of Lipid A: INSIGHTS TO POLYSPECIFICITY TOWARD SINGLE-STRANDED DNA.

Haji-Ghassemi, O.Muller-Loennies, S.Rodriguez, T.Brade, L.Kosma, P.Brade, H.Evans, S.V.

(2015) J.Biol.Chem. 290: 19629-19640

  • DOI: 10.1074/jbc.M115.657874
  • Primary Citation of Related Structures:  4ODS, 4ODU, 4ODV, 4ODW, 4Z8F, 4Z95

  • PubMed Abstract: 
  • Septic shock is a leading cause of death, and it results from an inflammatory cascade triggered by the presence of microbial products in the blood. Certain LPS from Gram-negative bacteria are very potent inducers and are responsible for a high percen ...

    Septic shock is a leading cause of death, and it results from an inflammatory cascade triggered by the presence of microbial products in the blood. Certain LPS from Gram-negative bacteria are very potent inducers and are responsible for a high percentage of septic shock cases. Despite decades of research, mAbs specific for lipid A (the endotoxic principle of LPS) have not been successfully developed into a clinical treatment for sepsis. To understand the molecular basis for the observed inability to translate in vitro specificity for lipid A into clinical potential, the structures of antigen-binding fragments of mAbs S1-15 and A6 have been determined both in complex with lipid A carbohydrate backbone and in the unliganded form. The two antibodies have separate germ line origins that generate two markedly different combining-site pockets that are complementary both in shape and charge to the antigen. mAb A6 binds lipid A through both variable light and heavy chain residues, whereas S1-15 utilizes exclusively the variable heavy chain. Both antibodies bind lipid A such that the GlcN-O6 attachment point for the core oligosaccharide is buried in the combining site, which explains the lack of LPS recognition. Longstanding reports of polyspecificity of anti-lipid A antibodies toward single-stranded DNA combined with observed homology of S1-15 and A6 and the reports of several single-stranded DNA-specific mAbs prompted the determination of the structure of S1-15 in complex with single-stranded DNA fragments, which may provide clues about the genesis of autoimmune diseases such as systemic lupus erythematosus, thyroiditis, and rheumatic autoimmune diseases.


    Organizational Affiliation

    From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
S1-15 Fab (IgG2b) heavy chain
H
226N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
S1-15 Fab (IgG2b kappa) light chain
L
214N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG0
Query on PG0

Download SDF File 
Download CCD File 
H, L
2-(2-METHOXYETHOXY)ETHANOL
PEG 6000
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
 Ligand Interaction
Z9M
Query on Z9M

Download SDF File 
Download CCD File 
H
2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose
C6 H14 N O8 P
QWDBGVNDGYUIAC-QZABAPFNSA-N
 Ligand Interaction
GP1
Query on GP1

Download SDF File 
Download CCD File 
H
GLUCOSAMINE 1-PHOSPHATE
C6 H14 N O8 P
YMJBYRVFGYXULK-QZABAPFNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.197 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.471α = 90.00
b = 77.471β = 90.00
c = 156.205γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
PHASERphasing
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-24
    Type: Initial release
  • Version 1.1: 2015-07-01
    Type: Database references
  • Version 1.2: 2015-10-07
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Refinement description