4Z95

Fab structure of antibody S1-15 in complex with ssDNA DNA, 5'-5(dT)-p-3'

  • Classification: IMMUNE SYSTEM/DNA

  • Deposited: 2015-04-09 Released: 2015-06-24 
  • Deposition Author(s): Haji-Ghassemi, O., Evans, S.V.
  • Funding Organization(s): Natural Sciences and Engineering Research Council (Canada); FWF 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.4 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, 4ODT, 4ODU, 4ODV, 4ODW, 4Z8F

  • 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
227N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
S1-15 Fab (IgG2b) light chain
L
214N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
H
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.761α = 90.00
b = 77.761β = 90.00
c = 156.525γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data collection
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Natural Sciences and Engineering Research Council (Canada)CanadaOGP0171356
FWFAustriaP22909

Revision History 

  • Version 1.0: 2015-06-24
    Type: Initial release
  • Version 1.1: 2015-07-01
    Type: Database references
  • Version 1.2: 2015-08-26
    Type: Database references
  • Version 1.3: 2017-08-23
    Type: Data collection, Database references, Derived calculations
  • Version 1.4: 2017-09-27
    Type: Author supporting evidence