PDBsum entry 1k9u

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Allergen PDB id
Protein chains
76 a.a. *
SO4 ×3
_CA ×4
Waters ×157
* Residue conservation analysis
PDB id:
Name: Allergen
Title: Crystal structure of the calcium-binding pollen allergen phl p 7 (polcalcin) at 1.75 angstroem
Structure: Polcalcin phl p 7. Chain: a, b. Synonym: timothy grass pollen allergen phl p 7, p7. Engineered: yes
Source: Phleum pratense. Timothy grass. Organism_taxid: 15957. Gene: phlpr. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
1.75Å     R-factor:   0.192     R-free:   0.223
Authors: P.Verdino,K.Westritschnig,R.Valenta,W.Keller
Key ref:
P.Verdino et al. (2002). The cross-reactive calcium-binding pollen allergen, Phl p 7, reveals a novel dimer assembly. EMBO J, 21, 5007-5016. PubMed id: 12356717 DOI: 10.1093/emboj/cdf526
30-Oct-01     Release date:   30-Apr-03    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
O82040  (POLC7_PHLPR) -  Polcalcin Phl p 7
78 a.a.
76 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     metal ion binding     2 terms  


DOI no: 10.1093/emboj/cdf526 EMBO J 21:5007-5016 (2002)
PubMed id: 12356717  
The cross-reactive calcium-binding pollen allergen, Phl p 7, reveals a novel dimer assembly.
P.Verdino, K.Westritschnig, R.Valenta, W.Keller.
The timothy grass pollen allergen Phl p 7 assembles most of the IgE epitopes of a novel family of 2 EF-hand calcium-binding proteins and therefore represents a diagnostic marker allergen and vaccine candidate for immunotherapy. Here we report the first three-dimensional structure of a representative of the 2 EF-hand allergen family, Phl p 7, in the calcium-bound form. The protein occurs as a novel dimer assembly with unique features: in contrast to well known EF-hand proteins such as calmodulin, parvalbumin or the S100 proteins, Phl p 7 adopts an extended conformation. Two protein monomers assemble in a head-to-tail arrangement with domain-swapped EF-hand pairing. The intertwined dimer adopts a barrel-like structure with an extended hydrophobic cavity providing a ligand-binding site. Calcium binding acts as a conformational switch between an open and a closed dimeric form of Phl p 7. These findings are interesting in the context of lipid- and calcium-dependent pollen tube growth. Furthermore, the structure of Phl p 7 allows for the rational development of vaccine strategies for treatment of sensitized allergic patients.
  Selected figure(s)  
Figure 3.
Figure 3 (A) Stereo diagram of the (3F[o] - 2F[c]) electron density map at 1.75 Å resolution contoured at 1 around the 12 amino acid calcium-binding loop of AI (residues 13−24) with the calcium ion (yellow sphere) positioned in the middle. (B) The 7-fold coordination of the calcium ion by oxygen atoms (red) of asparagines or aspartic acids, a peptide carbonyl oxygen, a water molecule and a bidentate glutamic acid in the positions X Y Z -Y -X -Z according to the nomenclature of Kretsinger (Kretsinger and Nockolds, 1973; Lewit-Bentley and Rety, 2000). (C) The loop pairing interactions between AI (blue) and BII (red): two hydrogen bonds (green dotted lines) are formed between the peptide planes of I20 (chain A) and I55 (chain B). Furthermore, this short -sheet assembly is stabilized by hydrophobic interactions (red dotted lines) between the side chains of I20 and I55 as well as K19 and F54. The latter residues are also involved in the calcium coordination via their backbone carbonyl oxygen atoms [in position -Y in (B)].
Figure 5.
Figure 5 (A) Intersection through the Phl p 7 dimer. The polypeptide backbone is represented in light grey. Surfaces were calculated and coloured according to their hydrophobicity, from brown (hydrophobic) through green to blue (hydrophilic) with SYBYL® 6.7.1 (Tripos Inc.). The protein's outer surface is hydrophilic (especially in the calcium-binding regions), whereas the cavity is predominantly hydrophobic and completely sealed by hydrophobic side chains. (B) Zooming into the hydrophobic cavity: the (3F[o] - 2F[c]) electron density contoured at 1 of the ligand (blue map) surrounded by the lining residues. Eight isoleucine, eight leucine, two alanine and one valine residue comprise the lateral walls of the cavity, whereas clusters of phenylalanine residues form the top and the bottom. The only polar side chain within the hydrophobic assembly, an aspartic acid coordinating a solvent molecule, is located in the more globular upper part of the cavity. (C and D) Surface plots of key features of the Phl p 7 dimer assembly: the ridge evolving at the 'kink' region and the calcium-coordinating site AI/BII. The left pictures represent the polypeptide backbones of chain A (blue) and chain B (red). The electrostatic potential distribution coloured from red (negative) through white to blue (positive) with GRASP (Nicholls et al., 1991) is shown in the middle. The right pictures show the surface hydrophobicity that is colour-coded analogously to (A).
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 5007-5016) copyright 2002.  
  Figures were selected by the author.  
    Author's comment    
  The 3D structure of the Phl p 7 allergen yielded the basis for a point mutation and a fragmentation approach leading to hypo-allergenic derivatives (see Westritschnig et al. (2004) Generation of an allergy vaccine by disruption of the three-dimensional structure of the cross-reactive calcium-binding allergen, Phl p 7. J. Immunol., 172, 5684-5692. [PubMedi d: 15100313], [Full text]).  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19960453 A.Harrer, M.Egger, G.Gadermaier, A.Erler, M.Hauser, F.Ferreira, and M.Himly (2010).
Characterization of plant food allergens: an overview on physicochemical and immunological techniques.
  Mol Nutr Food Res, 54, 93.  
20553495 I.Magler, D.Nüss, M.Hauser, F.Ferreira, and H.Brandstetter (2010).
Molecular metamorphosis in polcalcin allergens by EF-hand rearrangements and domain swapping.
  FEBS J, 277, 2598-2610.  
  20298513 M.Hauser, A.Roulias, F.Ferreira, and M.Egger (2010).
Panallergens and their impact on the allergic patient.
  Allergy Asthma Clin Immunol, 6, 1.  
19864426 T.Oda, H.Hashimoto, N.Kuwabara, S.Akashi, K.Hayashi, C.Kojima, H.L.Wong, T.Kawasaki, K.Shimamoto, M.Sato, and T.Shimizu (2010).
Structure of the N-terminal regulatory domain of a plant NADPH oxidase and its functional implications.
  J Biol Chem, 285, 1435-1445.
PDB code: 3a8r
18627309 K.Schweimer, A.Petersen, R.Suck, W.M.Becker, P.Rösch, and I.Matecko (2008).
Solution structure of Phl p 3, a major allergen from timothy grass pollen.
  Biol Chem, 389, 919-923.
PDB code: 2jnz
17910695 M.Grote, V.Krzyzanek, and R.Reichelt (2007).
Bundles of hexagonally arranged tubules in timothy grass pollen: detection of a novel pollen component using anhydrous fixation and image analysis techniques in transmission electron microscopy.
  J Microsc, 228, 34-39.  
16512810 A.Ledesma, R.Barderas, K.Westritschnig, J.Quiralte, C.Y.Pascual, R.Valenta, M.Villalba, and R.Rodríguez (2006).
A comparative analysis of the cross-reactivity in the polcalcin family including Syr v 3, a new member from lilac pollen.
  Allergy, 61, 477-484.  
16700049 C.A.Bottoms, T.A.White, and J.J.Tanner (2006).
Exploring structurally conserved solvent sites in protein families.
  Proteins, 64, 404-421.  
16475895 N.Mothes, R.Valenta, and S.Spitzauer (2006).
Allergy testing: the role of recombinant allergens.
  Clin Chem Lab Med, 44, 125-132.  
15937283 D.V.Venkitaramani, D.B.Fulton, A.H.Andreotti, K.M.Johansen, and J.Johansen (2005).
Solution structure and backbone dynamics of Calsensin, an invertebrate neuronal calcium-binding protein.
  Protein Sci, 14, 1894-1901.
PDB codes: 1yx7 1yx8
15634345 T.Ball, W.Edstrom, L.Mauch, J.Schmitt, B.Leistler, H.Fiebig, W.R.Sperr, A.W.Hauswirth, P.Valent, D.Kraft, S.C.Almo, and R.Valenta (2005).
Gain of structure and IgE epitopes by eukaryotic expression of the major Timothy grass pollen allergen, Phl p 1.
  FEBS J, 272, 217-227.  
15130477 M.A.Schumacher, M.Crum, and M.C.Miller (2004).
Crystal structures of apocalmodulin and an apocalmodulin/SK potassium channel gating domain complex.
  Structure, 12, 849-860.
PDB codes: 1qx5 1qx7
15640701 P.L.Bhalla, and M.B.Singh (2004).
Engineered allergens for immunotherapy.
  Curr Opin Allergy Clin Immunol, 4, 569-573.  
12966101 C.Siebold, I.Arnold, L.F.Garcia-Alles, U.Baumann, and B.Erni (2003).
Crystal structure of the Citrobacter freundii dihydroxyacetone kinase reveals an eight-stranded alpha-helical barrel ATP-binding domain.
  J Biol Chem, 278, 48236-48244.
PDB codes: 1un8 1un9
12413521 R.Valenta, and D.Kraft (2002).
From allergen structure to new forms of allergen-specific immunotherapy.
  Curr Opin Immunol, 14, 718-727.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.