8SHW | pdb_00008shw

38B7 with hydroxy-proline peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.205 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structural determinants of peanut induced anaphylaxis.

Smith, S.A.Shrem, R.A.Lanca, B.B.C.Zhang, J.Wong, J.J.W.Croote, D.Peebles Jr., R.S.Spiller, B.W.

(2025) J Allergy Clin Immunol 

  • DOI: https://doi.org/10.1016/j.jaci.2024.12.1095
  • Primary Citation of Related Structures:  
    8SHV, 8SHW, 8SI1, 8SJ4, 8SJ6, 8SJA

  • PubMed Abstract: 

    Human monoclonal IgE antibodies recognizing peanut allergens have recently become available, but we lack a detailed understanding of how these IgEs target allergens. To determine the molecular details of the antibody-allergen interaction for a panel of clinically important human IgE monoclonal antibodies and to develop strategies to disrupt disease causing antibody-allergen interactions. We identified candidates from a panel of epitope binned human IgE monoclonals that recognize two important and homologous peanut allergens, Ara h 2 and Ara h 6. Crystal structures were determined revealing the interfaces (antigenic sites) of exemplars of five common IgE bins. Among the common antigenic sites on Ara h 2 and Ara h 6, two sites (A and B) are highly conserved between the allergens, explaining the cross reactivity of antibodies that recognize these sites. Three sites (C, D, and F) involve residues that are not conserved between the allergens. Of the five common sites, three Sites (B, C, and D) involve residues that are only near each other when the allergens are properly folded, such that these sites are conformational. Two additional sites (sites A and F) involve largely linear stretches of amino acids. Site F targeted antibody, 38B7, binds to a peptide sequence DPYSP OH S, in which hydroxylation of the last proline is critical for binding. This sequence is repeated two or three times depending on the Ara h 2 isoform, enabling 38B7 to induce anaphylaxis as a single monoclonal, without a second antibody. We have mutated key residues in each site and created a panel of hypoallergens, having reduced IgE mAb binding and lacking the ability to induce anaphylaxis in our murine model. We created a structural map of the IgE antibody response to the most important peanut allergen proteins to enable the design of new allergy immunotherapies and vaccines.


  • Organizational Affiliation
    • Department of Medicine, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
38B7 light chainA [auth L],
C [auth A]
215Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
38B7 heavy chainB [auth H],
D [auth C]
221Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Conglutin-7E [auth Q],
F [auth B]
14Arachis hypogaeaMutation(s): 0 
UniProt
Find proteins for Q6PSU2 (Arachis hypogaea)
Explore Q6PSU2 
Go to UniProtKB:  Q6PSU2
Entity Groups  
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UniProt GroupQ6PSU2
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth D]4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
H [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HYP
Query on HYP
E [auth Q],
F [auth B]
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.205 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.021α = 90
b = 91.784β = 93.22
c = 82.946γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata processing
pointlessdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United States5R01AI155668

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-01-29
    Changes: Database references