1Q9B | pdb_00001q9b

CRYSTAL STRUCTURE ANALYSIS OF Hev b 6.02 (HEVEIN) AT 1.5 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.145 (Depositor), 0.141 (DCC) 
  • R-Value Work: 
    0.137 (DCC) 
  • R-Value Observed: 
    0.128 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.6 of the entry. See complete history

Literature

Insights into a conformational epitope of Hev b 6.02 (hevein).

Reyes-Lopez, C.A.Hernandez-Santoyo, A.Pedraza-Escalona, M.Mendoza, G.Hernandez-Arana, A.Rodriguez-Romero, A.

(2004) Biochem Biophys Res Commun 314: 123-130

  • DOI: https://doi.org/10.1016/j.bbrc.2003.12.068
  • Primary Citation Related Structures: 
    1Q9B

  • PubMed Abstract: 

    Hevein (Hev b 6.02) is a major IgE-binding allergen in natural rubber latex and manufactured products. Both tryptophans (Trp(21) and Trp(23)) of the hevein molecule were chemically modified with BNPS-skatole (2-nitrophenylsulfenyl-3-methyl-3(')-bromoindolenine); derivatized allergen failed to significantly inhibit binding of serum IgE in ELISA assays. Similarly, skin prick tests showed that hevein-positive patients gave no response with the modified allergen. Dot blot experiments carried out with anti-hevein mono- and polyclonal antibodies confirmed the importance of Trp(21) and Trp(23) for antibody-recognition, and demonstrated the specific cross-reactivity of other molecules containing hevein-like domains. We also report the structure of Hev b 6.02 at an extended resolution (1.5A) and compare its surface properties around Trp residues with those of similar regions in other allergens. Overall our results indicate that the central part of the protein, which comprises three aromatic and other acidic and polar residues, constitutes a conformational epitope.


  • Organizational Affiliation
    • Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Cd. Universitaria, 04510, Coyoacán México, DF, Mexico.

Macromolecule Content 

  • Total Structure Weight: 4.97 kDa 
  • Atom Count: 416 
  • Modeled Residue Count: 43 
  • Deposited Residue Count: 43 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hevein43Hevea brasiliensisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P02877 (Hevea brasiliensis)
Explore P02877 
Go to UniProtKB:  P02877
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02877
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.145 (Depositor), 0.141 (DCC) 
  • R-Value Work:  0.137 (DCC) 
  • R-Value Observed: 0.128 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.81α = 90
b = 60.95β = 90
c = 22.51γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
SCALAdata scaling
Agrovatadata reduction
TRUNCATEdata reduction
CNSrefinement
DENZOdata reduction
CCP4data scaling
ROTAVATAdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2024-11-20
    Changes: Structure summary