1ELP

GAMMA-D CRYSTALLIN STRUCTURE AT 1.95 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Work: 0.204 

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This is version 1.2 of the entry. See complete history


Literature

Structure of bovine eye lens gammaD (gammaIIIb)-crystallin at 1.95 A.

Chirgadze, Y.N.Driessen, H.P.Wright, G.Slingsby, C.Hay, R.E.Lindley, P.F.

(1996) Acta Crystallogr D Biol Crystallogr 52: 712-721

  • DOI: 10.1107/S0907444996000352
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of bovine lens gammaIIIb-crystallin at 2.5 A resolution previously reported was interpreted using a consensus sequence derived from related vertebrate sequences on the assumption that gammaIIIb-crystallin derived from the gammaC ...

    The crystal structure of bovine lens gammaIIIb-crystallin at 2.5 A resolution previously reported was interpreted using a consensus sequence derived from related vertebrate sequences on the assumption that gammaIIIb-crystallin derived from the gammaC-crystallin gene. It has recently been shown that gammaIIIb is a product of the bovine gammaD gene. The structure of gammaIIIb has now been refined with the bovine gammaD sequence using new 1.95 A resolution synchrotron data. The crystallographic R factor was 20.4% for all 33 104 reflection data between 8.0 and 1.95 A measured at 277(1) K. The electron density fully supported the assignment of the gammaD sequence to gammaIIIb. The crystal belongs to space group P2(1)2(1)2(1) with two molecules of molecular mass 20 749 Da in the asymmetric unit in which 219 water molecules were located. The two-domain four-Greek-key motif highly symmetrical protein is very similar in structure to gammaB-crystallin (81% sequence identity). There is a single amino-acid deletion in gammaD in the linker region connecting the two domains. The intermolecular oganization in the crystal lattice is quite different from gammaB as a result of key mutations involving surface residues Leu51, Ile103 and His155. These point mutations will contribute to the intermolecular behaviour of the gamma-crystallins in the eye lens, where they are major components of the densely packed, high refractive index regions of the lens.


    Related Citations: 
    • Crystal Structure of Calf Eye Lens Gamma-Crystallin Iiib at 2.5 A Resolution: Its Relation to Function
      Chirgadze, Yu., Nevskaya, N., Vernoslova, E., Nikonov, S., Sergeev, Yu., Brazhnikov, E., Fomenkova, N., Lunin, V., Urzhumtsev, A.
      (1991) Exp Eye Res 53: 295
    • 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 4: 137
    • [the Key Role of the Residue 103 in the Surface Interactions of Gamma-Crystallins]
      Sergeev, Iu.V., Chirgadze, Iu.N., Driessen, H., Slingsby, C., Blundell, T.L.
      (1987) Mol Biol (Mosk) 21: 377
    • 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 21: 317
    • Spatial Structure of Gamma-Crystallin Iiib from Calf Eye Lens at 2.5 Angstroms Resolution
      Chirgadze, Yu.N., Nevskaya, N.A., Fomenkova, N.P., Nikonov, S.V., Sergeev, Yu.V., Brazhnikov, E.V., Garber, M.B., Lunin, V.Yu., Urzumtsev, A.P., Vernoslova, E.A.
      (1986) Dokl Akad Nauk SSSR 290: 492
    • Phase Improvement in Protein Crystallography Using a Mixed Electron Density Model
      Lunin, V.Yu., Urzhumtsev, A.G., Vernoslova, E.A., Chirgadze, Yu.N., Nevskaya, N.A., Fomenkova, N.P.
      (1985) Acta Crystallogr A 41: 166
    • Improvement of Protein Phases by Coarse Model Modification
      Lunin, V.Yu., Urzhumtsev, A.G.
      (1984) Acta Crystallogr A 40: 269
    • Structure of Gamma-Crystallin Iiib from the Eye Lens of the Calf at 3 Angstroms Resolution
      Chirgadze, Yu.N., Sergeev, Yu.V., Fomenkova, N.P., Oreshin, V.D., Nikonov, S.V.
      (1981) Dokl Akad Nauk SSSR 259: 1502
    • Polypeptide Chain Pathway in Gamma-Crystallin Iiib from Calf Lens at 3 A Resolution
      Chirgadze, Yu.N., Sergeev, Yu.V., Fomenkova, N.P., Oreshin, V.D.
      (1981) FEBS Lett 131: 81
    • Structure of Gamma-Crystallin Iiib from Calf Lens at 5 A Resolution
      Chirgadze, Y.N., Oreshin, V.D., Sergeev, Y.V., Nikonov, S.V., Lunin, V.Y.
      (1980) FEBS Lett 118: 296
    • 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
    • Growing Single Crystals of Gamma Crystallin from the Calf Crystalline Lens
      Garber, M.B., Reshetnikova, L.S.
      (1976) Dokl Akad Nauk SSSR 226: 1452

    Organizational Affiliation

    Laboratory of Structure Analysis, Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GAMMA-D CRYSTALLIN
A, B
173Bos taurusMutation(s): 0 
Gene Names: CRYGD
Find proteins for P08209 (Bos taurus)
Go to UniProtKB:  P08209
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.81α = 90
b = 70.03β = 90
c = 117.25γ = 90
Software Package:
Software NamePurpose
RESTRAINrefinement
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-06-10
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance