4A85

Crystal Structure of Major Birch Pollen Allergen Bet v 1 a in complex with kinetin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.122 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Crystallographically Mapped Ligand Binding Differs in High and Low Ige Binding Isoforms of Birch Pollen Allergen Bet V 1.

Kofler, S.Asam, C.Eckhard, U.Wallner, M.Ferreira, F.Brandstetter, H.

(2012) J Mol Biol 422: 109

  • DOI: https://doi.org/10.1016/j.jmb.2012.05.016
  • Primary Citation of Related Structures:  
    4A80, 4A81, 4A83, 4A84, 4A85, 4A86, 4A87, 4A88, 4A8G, 4A8U, 4A8V

  • PubMed Abstract: 

    The ability of pathogenesis-related proteins of family 10 to bind a broad spectrum of ligands is considered to play a key role for their physiological and pathological functions. In particular, Bet v 1, an archetypical allergen from birch pollen, is described as a highly promiscuous ligand acceptor. However, the detailed recognition mechanisms, including specificity factors discriminating binding properties of naturally occurring Bet v 1 variants, are poorly understood. Here, we report crystal structures of Bet v 1 variants in complex with an array of ligands at a resolution of up to 1.2 Å. Residue 30 within the hydrophobic pocket not only discriminates in high and low IgE binding Bet v 1 isoforms but also induces a drastic change in the binding mode of the model ligand deoxycholate. Ternary crystal structure complexes of Bet v 1 with several ligands together with the fluorogenic reporter 1-anilino-8-naphthalene sulfonate explain anomalous fluorescence binding curves obtained from 1-anilino-8-naphthalene sulfonate displacement assays. The structures reveal key interaction residues such as Tyr83 and rationalize both the binding specificity and promiscuity of the so-called hydrophobic pocket in Bet v 1. The intermolecular interactions of Bet v 1 reveal an unexpected complexity that will be indispensable to fully understand its roles within the physiological and allergenic context.


  • Organizational Affiliation

    Structural Biology Group, Department of Molecular Biology, University of Salzburg, A-5020 Salzburg, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MAJOR POLLEN ALLERGEN BET V 1-A159Betula pendulaMutation(s): 0 
UniProt
Find proteins for P15494 (Betula pendula)
Explore P15494 
Go to UniProtKB:  P15494
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15494
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H35
Query on H35

Download Ideal Coordinates CCD File 
B [auth A]N-(FURAN-2-YLMETHYL)-7H-PURIN-6-AMINE
C10 H9 N5 O
QANMHLXAZMSUEX-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
H [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD
Query on MPD

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.122 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.69α = 90
b = 55.89β = 93.24
c = 38.04γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2012-08-15
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description