4Z8F

Fab structure of antibody S1-15 in complex with ssDNA DNA, 5'-p5(dT)p-3'

• PDB DOI:  https://doi.org/10.2210/pdb4Z8F/pdb
• NAKB: 4Z8F

• Classification: IMMUNE SYSTEM/DNA
• Organism(s): Mus musculus, synthetic construct
• Mutation(s): No 


• Deposited: 2015-04-08 Released: 2015-06-24 
• Deposition Author(s): Haji-Ghassemi, O., Evans, S.V.
• Funding Organization(s): FWF, Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.240 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 

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

• PubMed: 26085093 
• DOI: https://doi.org/10.1074/jbc.M115.657874
• Primary Citation of Related Structures:  
  4ODS, 4ODT, 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 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.

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Organizational Affiliation: 

From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada, [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 51.28 kDa 
• Atom Count: 3,684 
• Modelled Residue Count: 447 
• Deposited Residue Count: 451 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S1-15 Fab (IgG2b) heavy chain	A [auth H]	227	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S1-15 Fab (IgG2b kappa) light chain	B [auth L]	214	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(P*TP*TP*TP*TP*T)-3'	C [auth E], D [auth A]	5	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.240 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.585	α = 90
b = 77.585	β = 90
c = 156.267	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-06-24 
Deposition Author(s): Haji-Ghassemi, O., Evans, S.V.

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Funding Organization	Location	Grant Number
FWF	Austria	P22909
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	OGP0171356

Revision History  

• Version 1.0: 2015-06-24
  Type: Initial release
  
• Version 1.1: 2015-07-01
  Changes: Database references
• Version 1.2: 2015-08-26
  Changes: Database references
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2020-01-08
  Changes: Author supporting evidence
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Refinement description