1HK0

Human GammaD Crystallin Structure at 1.25 A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

High-Resolution X-Ray Crystal Structures of Human Gammad Crystallin (1.25A) and the R58H Mutant (1.15A) Associated with Aculeiform Cataract

Basak, A.K.Bateman, O.Slingsby, C.Pande, A.Asherie, N.Ogun, O.Benedek, G.Pande, J.

(2003) J Mol Biol 328: 1137-1147

  • DOI: 10.1016/s0022-2836(03)00375-9
  • Primary Citation of Related Structures:  
    1H4A, 1HK0

  • PubMed Abstract: 
  • Several human cataracts have been linked to mutations in the gamma crystallin gene. One of these is the aculeiform cataract, which is caused by an R58H mutation in gammaD crystallin. We have shown previously that this cataract is caused by crystallization of the mutant protein, which is an order of magnitude less soluble than the wild-type ...

    Several human cataracts have been linked to mutations in the gamma crystallin gene. One of these is the aculeiform cataract, which is caused by an R58H mutation in gammaD crystallin. We have shown previously that this cataract is caused by crystallization of the mutant protein, which is an order of magnitude less soluble than the wild-type. Here, we report the very high-resolution crystal structures of the mutant and wild-type proteins. Both proteins crystallize in the same space group and lattice. Thus, a strict comparison of the protein-protein and protein-water intermolecular interactions in the two crystal lattices is possible. Overall, the differences between the mutant and wild-type structures are small. At position 58, the mutant protein loses the direct ion-pair intermolecular interaction present in the wild-type, due to the differences between histidine and arginine at the atomic level; the interaction in the mutant is mediated by water molecules. Away from the mutation site, the mutant and wild-type lattice structures differ in the identity of side-chains that occupy alternate conformations. Since the interactions in the crystal phase are very similar for the two proteins, we conclude that the reduction in the solubility of the mutant is mainly due to the effect of the R58H mutation in the solution phase. The results presented here are also important as they are the first high-resolution X-ray structures of human gamma crystallins.


    Related Citations: 
    • Crystal Structure of Calf Eye Lens Gamma-Crystallin Iiib at 2.5 A Resolution: Its Relation to Function
      Yu, C., Nevskaya, N., Vernoslova, E., Nikonov, S., Yu, S., Brazhnikov, E., Fomenkova, N., Lunin, V., Urzhumtsev, A.
      (1991) Exp Eye Res 53: 295

    Organizational Affiliation

    Department of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma-crystallin DA [auth X]173Homo sapiensMutation(s): 0 
Gene Names: CRYGDCRYG4
UniProt & NIH Common Fund Data Resources
Find proteins for P07320 (Homo sapiens)
Explore P07320 
Go to UniProtKB:  P07320
PHAROS:  P07320
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07320
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.22α = 90
b = 52.971β = 90
c = 90.468γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-12-12
    Changes: Data collection, Database references, Experimental preparation, Source and taxonomy, Structure summary