8G4P

Crystal structure of the peanut allergen Ara h 2 bound by two neutralizing antibodies 13T1 and 13T5

PDB DOI: https://doi.org/10.2210/pdb8G4P/pdb

Classification: ALLERGEN
Organism(s): Homo sapiens, Arachis hypogaea
Expression System: Cricetulus griseus, Escherichia coli
Mutation(s): No

Deposited: 2023-02-10 Released: 2023-12-20
Deposition Author(s): Pedersen, L.C., Mueller, G.A., Min, J.
Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.217
R-Value Work: 0.189
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Design of an Ara h 2 hypoallergen from conformational epitopes.

Min, J., Keswani, T., LaHood, N.A., Lytle, I.R., Marini-Rapoport, O., Andrieux, L., Sneed, S.L., Edwards, L.L., Petrovich, R.M., Perera, L., Pomes, A., Pedersen, L.C., Patil, S.U., Mueller, G.A.

(2024) Clin Exp Allergy 54: 46-55

PubMed: 38168500 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1111/cea.14433
Primary Citation of Related Structures:
8G4P

PubMed Abstract:
Adverse reactions are relatively common during peanut oral immunotherapy. To reduce the risk to the patient, some researchers have proposed modifying the allergen to reduce IgE reactivity, creating a putative hypoallergen. Analysis of recently cloned human IgG from patients treated with peanut immunotherapy suggested that there are three common conformational epitopes for the major peanut allergen Ara h 2. We sought to test if structural information on these epitopes could indicate mutagenesis targets for designing a hypoallergen and evaluated the reduction in IgE binding via immunochemistry and a mouse model of passive cutaneous anaphylaxis (PCA).

Organizational Affiliation

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, North Carolina, USA.

Macromolecule Content

Total Structure Weight: 113.68 kDa
Atom Count: 7,467
Modelled Residue Count: 967
Deposited Residue Count: 1,028
Unique protein chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
13t1 Fab heavy chain	A [auth C]	231	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
13T1 Fab light chain	B [auth D]	216	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
13T5 Fab heavy chain	C [auth A]	232	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
13T5 Fab light chain	D [auth B]	214	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Ara h 2 allergen	E	135	Arachis hypogaea	Mutation(s): 0 Gene Names: Ara h 2
UniProt
Find proteins for A0A445BYI5 (Arachis hypogaea) Explore A0A445BYI5 Go to UniProtKB: A0A445BYI5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A445BYI5
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Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain H [auth C] SDF format, chain K [auth D] SDF format, chain W [auth E] MOL2 format, chain V [auth B] MOL2 format, chain H [auth C] MOL2 format, chain K [auth D] MOL2 format, chain W [auth E]	H [auth C], K [auth D], V [auth B], W [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth C] Focus chain K [auth D] Focus chain V [auth B] Focus chain W [auth E] Interactions & Density Focus chain H [auth C] Focus chain K [auth D] Focus chain V [auth B] Focus chain W [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain F [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain S [auth B] SDF format, chain U [auth B] MOL2 format, chain R [auth B] MOL2 format, chain F [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B]	F [auth C] M [auth A] N [auth A] R [auth B] S [auth B] F [auth C], M [auth A], N [auth A], R [auth B], S [auth B], U [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth B] Interactions & Density Focus chain F [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain G [auth C] SDF format, chain I [auth D] SDF format, chain J [auth D] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain T [auth B] MOL2 format, chain O [auth A] MOL2 format, chain G [auth C] MOL2 format, chain I [auth D] MOL2 format, chain J [auth D] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain T [auth B]	G [auth C] I [auth D] J [auth D] O [auth A] P [auth A] G [auth C], I [auth D], J [auth D], O [auth A], P [auth A], Q [auth A], T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth C] Focus chain I [auth D] Focus chain J [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain T [auth B] Interactions & Density Focus chain G [auth C] Focus chain I [auth D] Focus chain J [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.217
R-Value Work: 0.189
R-Value Observed: 0.190
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.302	α = 90
b = 136.794	β = 127.34
c = 96.819	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-20

Deposition Author(s):

Pedersen, L.C.

Mueller, G.A.

Min, J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	1ZIAES102906
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	1ZICES102645

Revision History (Full details and data files)

Version 1.0: 2023-12-20
Type: Initial release
Version 1.1: 2024-01-17
Changes: Database references
Version 1.2: 2024-01-31
Changes: Database references

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Help and Resources

8G4P

Crystal structure of the peanut allergen Ara h 2 bound by two neutralizing antibodies 13T1 and 13T5

Design of an Ara h 2 hypoallergen from conformational epitopes.

Entity ID: 1

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Entity ID: 2

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Entity ID: 3

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Entity ID: 4

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Entity ID: 5

UniProt

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)