1H4A

HUMAN GAMMA-D CRYSTALLIN R58H MUTANT STRUCTURE AT 1.15 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • Primary Citation of Related Structures:  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 crystalliz ...

    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: 
    • Phase Improvement in Protein Crystallography Using a Mixed Electron Density Model
      Lunin Yu, V.,Urzhumtsev, A.G.,Vernoslova, E.A.,Chirgadze Yu, N.,Nevskaya, N.A.,Fomenkova, N.P.
      (1985) Acta Crystallogr.,Sect.A 41: 166
    • Crystallographic Study of Gamma-Crystallins from Calf Lens
      Chirgadze, Y.N.,Nikonov, S.V.,Garber, M.B.,Reshetnikova, L.S.
      (1977) J.Mol.Biol. 110: 619
    • Key Role of Residue 103 in Surface Interactions of Gamma-Crystallins
      Sergeev Yu, V.,Chirgadze Yu, N.,Driessen, H.,Slingsby, C.,Blundell, T.L.
      (1987) Mol.Biol.(Engl.Transl.) 21: 377
    • Surface Interactions of Gamma-Crystallins in the Crystal Medium in Relation to Their Association in the Eye Lens
      Sergeev, Y.V.,Chirgadze, Y.N.,Mylvaganam, S.E.,Driessen, H.,Slingsby, C.,Blundell, T.L.
      (1988) Proteins: Struct.,Funct., Genet. 4: 137
    • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GAMMA CRYSTALLIN D
X
173Homo sapiensGene Names: CRYGD (CRYG4)
Find proteins for P07320 (Homo sapiens)
Go to Gene View: CRYGD
Go to UniProtKB:  P07320
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 33.467α = 90.00
b = 53.234β = 90.00
c = 89.809γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance