5Y2E | pdb_00005y2e

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

• PDB DOI: https://doi.org/10.2210/pdb5Y2E/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Bovine rotavirus strain NCDV/G6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-07-25 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.274 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

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

• PubMed: 29455326 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 23 kDa 
• Atom Count: 1,403 
• Modelled Residue Count: 182 
• Deposited Residue Count: 188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural glycoprotein 4	A [auth D], B [auth A], C, D [auth B]	47	Bovine rotavirus strain NCDV/G6	Mutation(s): 1
UniProt
Find proteins for P08434 (Rotavirus A (strain RVA/Cow/United States/NCDV-Lincoln/1969/G6P6[1])) Explore P08434  Go to UniProtKB:  P08434

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.274 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.35	α = 90
b = 48.14	β = 90
c = 122.61	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-03-14 
Deposition Author(s): Suguna, K., Kumar, S.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT) Indian Institute of Science, (IISc) Partnership Program for Advanced Research in Biological Sciences and Bioengineering	India	--

Revision History  

• 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