5Y2J

Crystal structure of the oligomerization domain of NSP4 from rotavirus strain MF66

  • Classification: VIRAL PROTEIN
  • Organism(s): Bovine rotavirus G10
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2017-07-26 Released: 2018-03-14 
  • Deposition Author(s): Suguna, K., Kumar, S.
  • Funding Organization(s): Department of Biotechnology (DBT), Indian Institute of Science, (IISc) Partnership Program for Advanced Research in Biological Sciences and Bioengineering

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

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Literature

New tetrameric forms of the rotavirus NSP4 with antiparallel helices.

Kumar, S., Ramappa, R., Pamidimukkala, K., Rao, C.D., Suguna, K.

(2018) Arch Virol 163: 1531-1547

  • DOI: https://doi.org/10.1007/s00705-018-3753-6
  • Primary Citation of Related Structures:  
    5Y2E, 5Y2H, 5Y2J

  • PubMed Abstract: 

    Rotavirus nonstructural protein 4, the first viral enterotoxin to be identified, is a multidomain, multifunctional glycoprotein. Earlier, we reported a Ca 2+ -bound coiled-coil tetrameric structure of the diarrhea-inducing region of NSP4 from the rotavirus strains SA11 and I321 and a Ca 2+ -free pentameric structure from the rotavirus strain ST3, all with a parallel arrangement of α-helices. pH was found to determine the oligomeric state: a basic pH favoured a tetramer, whereas an acidic pH favoured a pentamer. Here, we report two novel forms of the coiled-coil region of NSP4 from the bovine rotavirus strains MF66 and NCDV. These crystallized at acidic pH, forming antiparallel coiled-coil tetrameric structures without any bound Ca 2+ ion. Structural and mutational studies of the coiled-coil regions of NSP4 revealed that the nature of the residue at position 131 (Tyr/His) plays an important role in the observed structural diversity.

    • Organizational Affiliation: 

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nonstructural protein 4
A, B, C, D
53Bovine rotavirus G10Mutation(s): 0 
UniProt
Find proteins for Q6QT01 (Bovine rotavirus G10)
Explore Q6QT01 
Go to UniProtKB:  Q6QT01
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6QT01
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.61α = 90
b = 69.57β = 90
c = 69.57γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata processing
Aimlessdata scaling
CRANK2phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT), Indian Institute of Science, (IISc) Partnership Program for Advanced Research in Biological Sciences and BioengineeringIndia--

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-05-30
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Derived calculations