4IAU

Atomic resolution structure of Geodin, a beta-gamma crystallin from Geodia cydonium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.129 
  • R-Value Work: 0.106 
  • R-Value Observed: 0.106 

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Literature

A novel interdomain interface in crystallins: structural characterization of the [beta][gamma]-crystallin from Geodia cydonium at 0.99 A resolution

Vergara, A.Grassi, M.Sica, F.Pizzo, E.D'Alessio, G.Mazzarella, L.Merlino, A.

(2013) Acta Crystallogr D Biol Crystallogr 69: 960-967

  • DOI: https://doi.org/10.1107/S0907444913003569
  • Primary Citation of Related Structures:  
    4IAU

  • PubMed Abstract: 

    The βγ-crystallin superfamily includes highly diverse proteins belonging to all of the kingdoms of life. Based on structural topology, these proteins are considered to be evolutionarily related to the long-lived βγ-crystallins that constitute the vertebrate eye lens. This study reports the crystallographic structure at 0.99 Å resolution of the two-domain βγ-crystallin (geodin) from the sponge Geodia cydonium. This is the most ancient member of the βγ-crystallin superfamily in metazoans. The X-ray structure shows that the geodin domains adopt the typical βγ-crystallin fold with a paired Greek-key motif, thus confirming the hypothesis that the crystallin-type scaffold used in the evolution of bacteria and moulds was recruited very early in metazoans. As a significant new structural feature, the sponge protein possesses a unique interdomain interface made up by pairing between the second motif of the first domain and the first motif of the second domain. The atomic resolution also allowed a detailed analysis of the calcium-binding site of the protein.


  • Organizational Affiliation

    Department of Chemical Sciences, University of Naples 'Federico II', Via Cintia, I-80126 Napoli, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-gamma-crystallin163Geodia cydoniumMutation(s): 0 
UniProt
Find proteins for O18426 (Geodia cydonium)
Explore O18426 
Go to UniProtKB:  O18426
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO18426
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.129 
  • R-Value Work: 0.106 
  • R-Value Observed: 0.106 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 24.17α = 90
b = 61.302β = 95.45
c = 50.175γ = 90
Software Package:
Software NamePurpose
SHELXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
SHELXLrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary