9GI7 | pdb_00009gi7

Hen Egg-White Lysozyme (HEWL) complexed with a Lindqvist-type hexavanadate (V6-OH) polyoxometalate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 
    0.218 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discrete Hybrid Vanadium-oxo Cluster as a Targeted Tool for Selective Protein Oxidative Modifications and Cleavage.

Moussawi, M.A.de Azambuja, F.Parac-Vogt, T.N.

(2025) Angew Chem Int Ed Engl 64: e202423078-e202423078

  • DOI: https://doi.org/10.1002/anie.202423078
  • Primary Citation of Related Structures:  
    9GI7

  • PubMed Abstract: 

    Understanding the impact of oxidative modification on protein structure and functions is essential for developing therapeutic strategies to combat macromolecular damage and cell death. However, selectively inducing oxidative modifications in proteins under physiological conditions remains challenging. Herein we demonstrate that [V 6 O 13 {(OCH 2 ) 3 CCH 2 OH} 2 ] 2- (V 6 -OH) hybrid metal-oxo cluster can be used for selective protein oxidative cleavage and modifications. We present the first example of a protein-bound hybrid vanadate cluster, where its interactions with protein surfaces and the redox activity of vanadium enable selective oxidative modifications. Single Crystal X-ray Diffraction (SC-XRD) of the V 6 -OH and hen egg white lysozyme (HEWL) complex revealed that the binding is dictated both by the inorganic core and the organic ligands attached to it. Selective oxidation or cleavage of HEWL occurs under physiological conditions by producing reactive oxygen species (ROS) in presence of ascorbate (Asc) as a reducing agent. The outcome of the oxidative reaction can be tuned by varying the concentration of V 6 -OH to result either in selective oxidation of the amino acid side chains or peptide bond cleavage. LC-MS and crystallography revealed that oxidative modifications were mainly concentrated near the cluster binding sites, providing spatial control of ROS production. This study advances our understanding of vanadium's role in biological systems and demonstrates the potential of hybrid metal-oxo clusters in protein modification.


  • Organizational Affiliation
    • Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001, Leuven, Belgium.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free:  0.218 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.723α = 90
b = 76.723β = 90
c = 35.954γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)Belgium1279721N

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-04-02
    Changes: Database references