4OIG

Dengue Virus Non-structural Protein NS1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of Flavivirus NS1 assembly and antibody recognition.

Edeling, M.A.Diamond, M.S.Fremont, D.H.

(2014) Proc.Natl.Acad.Sci.USA 111: 4285-4290

  • DOI: 10.1073/pnas.1322036111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Flavivirus nonstructural protein 1 (NS1) is a conserved, membrane-associated and secreted glycoprotein with replication and immune evasion functions. Secreted NS1 is a hexameric, barrel-shaped lipoprotein that can bind back to the plasma membrane ...

    The Flavivirus nonstructural protein 1 (NS1) is a conserved, membrane-associated and secreted glycoprotein with replication and immune evasion functions. Secreted NS1 is a hexameric, barrel-shaped lipoprotein that can bind back to the plasma membrane of cells. Antibodies targeting cell surface-associated NS1 can be protective in vivo in a manner dependent on Fc effector functions. We describe here the crystal structure of a C-terminal fragment (residues 172-352) of West Nile (WNV) and Dengue virus NS1 proteins at 1.85 and 2.7 Å resolution, respectively. NS1(172-352) assembles as a unique rod-shaped dimer composed of a 16-stranded β-platform flanked on one face by protruding connecting loops. We also determined the 3.0 Å resolution structure of WNV NS1(172-352) with the protective 22NS1 antibody Fab, which engages the loop-face of the rod. The head-to-head NS1(172-352) dimer we observe in crystal lattices is supported by multiangle light and small-angle X-ray scattering studies. We used the available cryo-electron microscopy reconstruction to develop a pseudoatomic model of the NS1 hexamer. The model was constructed with the NS1(172-352) dimeric rod aligned with the long axis of the barrel, and with the loop-face oriented away from the core. Difference densities suggest that the N-terminal region of NS1 forms globular lobes that mediate lateral contacts between dimers in the hexamer. Our model also suggests that the N-terminal lobe forms the surface of the central cavity where lipid binding may occur.


    Organizational Affiliation

    Departments of Pathology and Immunology, Medicine, Molecular Microbiology, and Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Non-structural protein 1, NS1
A, B, D, E
185Dengue virus type 1 (strain Nauru/West Pac/1974)Mutation(s): 0 
Find proteins for P17763 (Dengue virus type 1 (strain Nauru/West Pac/1974))
Go to UniProtKB:  P17763
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, D, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, D, E
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 109.175α = 90.00
b = 81.962β = 97.78
c = 97.189γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-04-02
    Type: Database references
  • Version 1.2: 2014-04-23
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Refinement description