Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18.30 kDa 
• Atom Count: 1612 
• Modelled Residue Count: 159 
• Deposited Residue Count: 159 
• Unique protein chains: 1

4BK7

Crystal Structure of a variant of the Major Birch Pollen Allergen Bet v 1

• PDB DOI: 10.2210/pdb4BK7/pdb

• Classification: ALLERGEN
• Organism(s): Betula pendula
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-04-22 Released: 2013-11-27 
• Deposition Author(s): Kofler, S., Brandstetter, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free: 0.175 
• R-Value Work: 0.134 
• R-Value Observed: 0.137 

Literature

Stabilization of the Dimeric Birch Pollen Allergen Bet V 1 Impacts its Immunological Properties

Kofler, S.G., Ackaert, C., Samonig, M., Asam, C., Briza, P., Horeis-Hoeck, J., Cabrele, C., Ferreira, F., Duschl, A., Huber, C., Brandstetter, H.

(2014) J Biol Chem 289: 540

• PubMed: 24253036 
• DOI: 10.1074/jbc.M113.518795
• Primary Citation of Related Structures:  
  4BK6, 4BK7, 4BKC, 4BKD


• PubMed Abstract: 
  

Many allergens share several biophysical characteristics, including the capability to undergo oligomerization. The dimerization mechanism in Bet v 1 and its allergenic properties are so far poorly understood. Here, we report crystal structures of dimeric Bet v 1, revealing a noncanonical incorporation of cysteine at position 5 instead of genetically encoded tyrosine. Cysteine polysulfide bridging stabilized different dimeric assemblies, depending on the polysulfide linker length. These dimers represent quaternary arrangements that are frequently observed in related proteins, reflecting their prevalence in unmodified Bet v 1. These conclusions were corroborated by characteristic immunologic properties of monomeric and dimeric allergen variants. Hereby, residue 5 could be identified as an allergenic hot spot in Bet v 1. The presented results refine fundamental principles in protein chemistry and emphasize the importance of protein modifications in understanding the molecular basis of allergenicity.

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Organizational Affiliation: 

From the Structural Biology Group, Department of Molecular Biology.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAJOR POLLEN ALLERGEN BET V 1-A	A	159	Betula pendula	Mutation(s): 1  Gene Names: BETVIA, BETVI
UniProt
Find proteins for P15494 (Betula pendula) Explore P15494  Go to UniProtKB:  P15494

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	G [auth A], H [auth A], I [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free: 0.175 
• R-Value Work: 0.134 
• R-Value Observed: 0.137 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.732	α = 90
b = 55.811	β = 93.25
c = 38.099	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-04-22 
• Released Date: 2013-11-27 
Deposition Author(s): Kofler, S., Brandstetter, H.

Revision History  

• Version 1.0: 2013-11-27
  Type: Initial release
  
• Version 1.1: 2014-01-15
  Changes: Database references