Crystal structure of Nitrollin, a betagamma-crystallin from Nitrosospira multiformis

Experimental Data Snapshot

  • Resolution: 1.86 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.181 

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Three-dimensional domain swapping in nitrollin, a single-domain betagamma-crystallin from Nitrosospira multiformis, controls protein conformation and stability but not dimerization

Aravind, P.Suman, S.K.Mishra, A.Sharma, Y.Sankaranarayanan, R.

(2009) J Mol Biol 385: 163-177

  • DOI: https://doi.org/10.1016/j.jmb.2008.10.035
  • Primary Citation of Related Structures:  
    3ENT, 3ENU

  • PubMed Abstract: 

    The betagamma-crystallin superfamily has a well-characterized protein fold, with several members found in both prokaryotic and eukaryotic worlds. A majority of them contain two betagamma-crystallin domains. A few examples, such as ciona crystallin and spherulin 3a exist that represent the eukaryotic single-domain proteins of this superfamily. This study reports the high-resolution crystal structure of a single-domain betagamma-crystallin protein, nitrollin, from the ammonium-oxidizing soil bacterium Nitrosospira multiformis. The structure retains the characteristic betagamma-crystallin fold despite a very low sequence identity. The protein exhibits a unique case of homodimerization in betagamma-crystallins by employing its N-terminal extension to undergo three-dimensional (3D) domain swapping with its partner. Removal of the swapped strand results in partial loss of structure and stability but not dimerization per se as determined using gel filtration and equilibrium unfolding studies. Overall, nitrollin represents a distinct single-domain prokaryotic member that has evolved a specialized mode of dimerization hitherto unknown in the realm of betagamma-crystallins.

  • Organizational Affiliation

    Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized protein114Nitrosospira multiformis ATCC 25196Mutation(s): 0 
Gene Names: 3786576
Find proteins for Q2YAE2 (Nitrosospira multiformis (strain ATCC 25196 / NCIMB 11849 / C 71))
Explore Q2YAE2 
Go to UniProtKB:  Q2YAE2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2YAE2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.86 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.257α = 90
b = 80.903β = 90
c = 32.137γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description