8BD0

Human Gamma-D crystallin R36S mutant with DTT-Cystein Protein modification


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

An ultraviolet-driven rescue pathway for oxidative stress to eye lens protein human gamma-D crystallin.

Hill, J.A.Nyathi, Y.Horrell, S.von Stetten, D.Axford, D.Owen, R.L.Beddard, G.S.Pearson, A.R.Ginn, H.M.Yorke, B.A.

(2024) Commun Chem 7: 81-81

  • DOI: https://doi.org/10.1038/s42004-024-01163-w
  • Primary Citation of Related Structures:  
    8BD0

  • PubMed Abstract: 

    Human gamma-D crystallin (HGD) is a major constituent of the eye lens. Aggregation of HGD contributes to cataract formation, the leading cause of blindness worldwide. It is unique in its longevity, maintaining its folded and soluble state for 50-60 years. One outstanding question is the structural basis of this longevity despite oxidative aging and environmental stressors including ultraviolet radiation (UV). Here we present crystallographic structures evidencing a UV-induced crystallin redox switch mechanism. The room-temperature serial synchrotron crystallographic (SSX) structure of freshly prepared crystallin mutant (R36S) shows no post-translational modifications. After aging for nine months in the absence of light, a thiol-adduct (dithiothreitol) modifying surface cysteines is observed by low-dose SSX. This is shown to be UV-labile in an acutely light-exposed structure. This suggests a mechanism by which a major source of crystallin damage, UV, may also act as a rescuing factor in a finely balanced redox system.


  • Organizational Affiliation

    School of Chemistry and Biosciences, University of Bradford, Richmond Road, Bradford, BD7 1DP, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Human Gamma-D Crystallin R36SA [auth X],
B [auth A]
171Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P07320 (Homo sapiens)
Explore P07320 
Go to UniProtKB:  P07320
PHAROS:  P07320
GTEx:  ENSG00000118231 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07320
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.9α = 90
b = 83.7β = 90
c = 101γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomSBF0061044

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-01
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Data collection
  • Version 1.2: 2024-05-15
    Changes: Database references