Crystal structure of vicilin from Corylus avellana (Hazelnut)

Experimental Data Snapshot

  • Resolution: 3.19 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

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Comparative study of 7S globulin from Corylus avellana and Solanum lycopersicum revealed importance of salicylic acid and Cu-binding loop in modulating their function.

Shikhi, M.Jain, A.Salunke, D.M.

(2020) Biochem Biophys Res Commun 522: 127-132

  • DOI: https://doi.org/10.1016/j.bbrc.2019.11.072
  • Primary Citation of Related Structures:  
    6L4C, 6L4M

  • PubMed Abstract: 

    The plant seed proteins referred to as vicilins belong to a structurally common superfamily. While some of them are reported to exhibit superoxide dismutase activity, vicilins from other sources do not possess this activity. Vicilin from Corylus avellana (HZ.1) and Solanum lycopersicum (SL80.1) were purified and subjected to structure-function analysis. The superoxide dismutase activity assays were performed to understand the functional differences between them. While SL80.1 has the superoxide dismutase activity, HZ.1 was enzymatically inactive. Crystal structure followed by mass spectrometry analysis of both the proteins revealed that while SL80.1 has bound salicylic acid, HZ.1 does not. Comparison of C-terminal binding pocket of both the structures revealed that a point mutation at residue 321 in HZ.1 (Gly→Cys) leads to obstruction in binding of salicylic acid in the pocket. Similarly, copper-binding loop of HZ.1 was reportedly found to be intact and shorter than the loops reported in SL80.1. The copper-binding loop of SL80.1 is rich in polar residues and the absence of these residues in HZ.1 copper-binding loop possibly indicates deficiency in channeling of oxygen radicals to the active center of the enzyme. Difference in the enzymatic activity of vicilin from two evolutionarily distinct sources is due to mutations in its co-factor binding pocket and copper-binding loop.

  • Organizational Affiliation

    Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121 001, India; Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
48-kDa glycoprotein
A, B, C
424Corylus avellanaMutation(s): 0 
Find proteins for Q8S4P9 (Corylus avellana)
Explore Q8S4P9 
Go to UniProtKB:  Q8S4P9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8S4P9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.19 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65α = 90
b = 91.137β = 90
c = 266.872γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description