7KYW | pdb_00007kyw

Crystal structure of timothy grass allergen Phl p 12.0101 reveals an unusual profilin dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.241 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.197 (Depositor) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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Literature

Crystal structure of timothy grass allergen Phl p 12.0101 reveals an unusual profilin dimer.

O'Malley, A.Kapingidza, A.B.Hyduke, N.Dolamore, C.Kowal, K.Chruszcz, M.

(2021) Acta Biochim Pol 68: 15-22

  • DOI: https://doi.org/10.18388/abp.2020_5587
  • Primary Citation Related Structures: 
    7KYW

  • PubMed Abstract: 

    Timothy grass pollen is a source of potent allergens. Among them, Phl p 1 and Phl p 5 are thought to be the most important, as a majority of timothy grass-allergic individuals have IgE antibodies directed against these two allergens. The profilin from timothy grass (Phl p 12) has been registered as a minor allergen, with up to 35% of individuals in populations of grass pollen allergic patients showing IgE binding to Phl p 12. Profilins are primarily minor allergens and are known for a high likelihood of co-sensitization as well as cross-reactivity situations caused by their sequence and structure similarity. The crystal structure of Phl p 12.0101 was determined and it revealed that this allergen may form an unusual dimer not previously observed among any profilins. For example, the Phl p 12 dimer has a completely different geometry and interface when compared with the latex profilin (Hev b 8) dimer that has its crystal structure determined. The structure of Phl p 12.0101 is described in the context of allergenic sensitization and allergy diagnostics. Moreover, the structure of the Phl p 12.0101 dimer is discussed, taking into account the production of recombinant allergens and their storage.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA.

Macromolecule Content 

  • Total Structure Weight: 14.37 kDa 
  • Atom Count: 1,029 
  • Modeled Residue Count: 131 
  • Deposited Residue Count: 131 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Profilin-1131Phleum pratenseMutation(s): 0 
Gene Names: PRO1PHLPXI
UniProt
Find proteins for P35079 (Phleum pratense)
Explore P35079 
Go to UniProtKB:  P35079
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35079
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT

Query on CIT



Download:Ideal Coordinates CCD File
B [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.241 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.197 (Depositor) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.344α = 90
b = 56.344β = 90
c = 94.379γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States2R01AI077653-10A1

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-31
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary