1G1J | pdb_00001g1j

CRYSTAL STRUCTURE OF THE OLIGOMERIZATION DOMAIN FROM ROTAVIRUS NSP4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 
    0.239 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the oligomerization domain of NSP4 from rotavirus reveals a core metal-binding site.

Bowman, G.D.Nodelman, I.M.Levy, O.Lin, S.L.Tian, P.Zamb, T.J.Udem, S.A.Venkataraghavan, B.Schutt, C.E.

(2000) J Mol Biology 304: 861-871

  • DOI: https://doi.org/10.1006/jmbi.2000.4250
  • Primary Citation Related Structures: 
    1G1I, 1G1J

  • PubMed Abstract: 

    During the maturation of rotaviral particles, non-structural protein 4 (NSP4) plays a critical role in the translocation of the immature capsid into the lumen of the endoplasmic reticulum. Full-length NSP4 and a 22 amino acid peptide (NSP4(114-135)) derived from this protein have been shown to induce diarrhea in young mice in an age-dependent manner, and may therefore be the agent responsible for rotavirally-induced symptoms. We have determined the crystal structure of the oligomerization domain of NSP4 which spans residues 95 to 137 (NSP4(95-137)). NSP4(95-137) self-associates into a parallel, tetrameric coiled-coil, with the hydrophobic core interrupted by three polar layers occupying a and d-heptad positions. Side-chains from two consecutive polar layers, consisting of four Gln123 and two of the four Glu120 residues, coordinate a divalent cation. Two independent structures built from MAD-phased data indicated the presence of a strontium and calcium ion bound at this site, respectively. This metal-binding site appears to play an important role in stabilizing the homo-tetramer, which has implications for the engagement of NSP4 as an enterotoxin.


  • Organizational Affiliation
    • Department of Molecular Biology, Lewis Thomas Laboratories, Princeton University, Princeton, NJ 08544, USA.

Macromolecule Content 

  • Total Structure Weight: 10.9 kDa 
  • Atom Count: 850 
  • Modeled Residue Count: 86 
  • Deposited Residue Count: 86 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NON-STRUCTURAL GLYCOPROTEIN NSP4
A, B
43N/AMutation(s): 1 
UniProt
Find proteins for P04512 (Rotavirus A (strain RVA/SA11-Both/G3P5B[2]))
Explore P04512 
Go to UniProtKB:  P04512
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04512
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SR

Query on SR



Download:Ideal Coordinates CCD File
C [auth B]STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.917α = 90
b = 35.908β = 90
c = 60.937γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary