Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 90 
  • Conformers Submitted: 25 
  • Selection Criteria: LOWEST ENERGY 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Solution Structure, Dynamics, and Hydrodynamics of the Calcium-Bound Cross-Reactive Birch Pollen Allergen Bet V 4 Reveal a Canonical Monomeric Two EF-Hand Assembly with a Regulatory Function

Neudecker, P.Nerkamp, J.Eisenmann, A.Nourse, A.Lauber, T.Schweimer, K.Lehmann, K.Schwarzinger, S.Ferreira, F.Roesch, P.

(2004) J Mol Biol 336: 1141

  • DOI: https://doi.org/10.1016/j.jmb.2003.12.070
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Birch pollinosis is one of the prevailing allergic diseases. In all, 5-20% of birch pollinotics mount IgE antibodies against the minor birch pollen allergen Bet v 4, a Ca2+-binding polcalcin. Due to IgE cross-reactivity among the polcalcins these patients are polysensitized to various plant pollens. Determination of the high-resolution structure of holo Bet v 4 by heteronuclear NMR spectroscopy reveals a canonical two EF-hand assembly in the open conformation with interhelical angles closely resembling holo calmodulin. The polcalcin-specific amphipathic COOH-terminal alpha-helix covers only a part of the hydrophobic groove on the molecular surface. Unlike the polcalcin Phl p 7 from timothy grass, which was recently shown to form a domain-swapped dimer, the hydrodynamic parameters from NMR relaxation, NMR translational diffusion, and analytical ultracentrifugation indicate that both apo and holo Bet v 4 are predominantly monomeric, raising the question of the physiological and immunological significance of the dimeric form of these polcalcins, whose physiological function is still unknown. The reduced helicity and heat stability in the CD spectra, the poor chemical shift dispersion of the NMR spectra, and the slightly increased hydrodynamic radius of apo Bet v 4 indicate a reversible structural transition upon Ca2+ binding, which explains the reduced IgE binding capacity of apo Bet v 4. The remarkable structural similarity of holo Bet v 4 and holo Phl p 7 in spite of different oligomerization states explains the IgE cross-reactivity and indicates that canonical monomers and domain-swapped dimers may be of similar allergenicity. Together with the close structural homology to calmodulin and the hydrophobic ligand binding groove this transition suggests a regulatory function for Bet v 4.

  • Organizational Affiliation

    Lehrstuhl für Biopolymere, Universität Bayreuth, D-95440 Bayreuth, Germany. philipp.neudecker@uni-bayreuth.de

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
POLCALCIN BET V 484Betula pendulaMutation(s): 0 
Find proteins for Q39419 (Betula pendula)
Explore Q39419 
Go to UniProtKB:  Q39419
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ39419
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 90 
  • Conformers Submitted: 25 
  • Selection Criteria: LOWEST ENERGY 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references, Derived calculations, Other