5JT8 | pdb_00005jt8

Structural basis for the limited antibody cross reactivity between the mite allergens Blo t 1 and Der p 1

• PDB DOI: https://doi.org/10.2210/pdb5JT8/pdb

• Classification: ALLERGEN
• Organism(s): Blomia tropicalis
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2016-05-09 Released: 2017-05-24 
• Deposition Author(s): Meno, K., Kastrup, J.S., Gajhede, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.170 (Depositor) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

The structure of the mite allergen Blo t 1 explains the limited antibody cross-reactivity to Der p 1.

Meno, K.H., Kastrup, J.S., Kuo, I.C., Chua, K.Y., Gajhede, M.

(2017) Allergy 72: 665-670

• PubMed: 27997997 
• DOI: https://doi.org/10.1111/all.13111
• Primary Citation Related Structures: 
  5JT8


• PubMed Abstract: 
  

  The Blomia tropicalis (Blo t) mite species is considered a storage mite in temperate climate zones and an important source of indoor allergens causing allergic asthma and rhinitis in tropical and subtropical regions. Here, we report the crystal structure of one of the allergens from Blo t, recombinant proBlo t 1 (rproBlo t 1), determined at 2.1 Å resolution. Overall, the fold of rproBlo t 1 is characteristic for the pro-form of cysteine proteases from the C1A class. Structural comparison of experimentally mapped Der f 1/Der p1 IgG epitopes to the same surface patch on Blo t 1, as well as of sequence identity of surface-exposed residues, suggests limited cross-reactivity between these allergens and Blo t 1. This is in agreement with ELISA inhibition results showing that, although cross-reactive human IgE epitopes exist, there are unique IgE epitopes for both Blo t 1 and Der p 1.

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Organizational Affiliation: 
• Global Research, ALK-Abelló A/S, Hørsholm, Denmark.
Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
Departments of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
Khoo Teck Puat-National University Children's Medical Institute, The National University Health System, Singapore.
Immunology Programme, Centre for Life Sciences, National University of Singapore, Singapore.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 77.6 kDa 
• Atom Count: 5,468 
• Modeled Residue Count: 622 
• Deposited Residue Count: 666 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Blo t 1 allergen	A, B	333	Blomia tropicalis	Mutation(s): 0  EC: 3.4.22
UniProt
Find proteins for A1KXI0 (Blomia tropicalis) Explore A1KXI0  Go to UniProtKB:  A1KXI0
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NO3	G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL	E [auth A], F [auth A], K [auth B], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.170 (Depositor) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.412	α = 90
b = 117.412	β = 90
c = 132.364	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-24 
Deposition Author(s): Meno, K., Kastrup, J.S., Gajhede, M.

Revision History  

• Version 1.0: 2017-05-24
  Type: Initial release
  
• Version 1.1: 2018-12-05
  Changes: Data collection, Database references
• Version 1.2: 2019-10-16
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary