6WEQ | pdb_00006weq

DENV1 NS1 in complex with neutralizing 2B7 Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.261 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6WEQ

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural basis for antibody inhibition of flavivirus NS1-triggered endothelial dysfunction.

Biering, S.B.Akey, D.L.Wong, M.P.Brown, W.C.Lo, N.T.N.Puerta-Guardo, H.Tramontini Gomes de Sousa, F.Wang, C.Konwerski, J.R.Espinosa, D.A.Bockhaus, N.J.Glasner, D.R.Li, J.Blanc, S.F.Juan, E.Y.Elledge, S.J.Mina, M.J.Beatty, P.R.Smith, J.L.Harris, E.

(2021) Science 371: 194-200

  • DOI: https://doi.org/10.1126/science.abc0476
  • Primary Citation Related Structures: 
    6WEQ, 6WER, 7K93

  • PubMed Abstract: 

    Medically important flaviviruses cause diverse disease pathologies and collectively are responsible for a major global disease burden. A contributing factor to pathogenesis is secreted flavivirus nonstructural protein 1 (NS1). Despite demonstrated protection by NS1-specific antibodies against lethal flavivirus challenge, the structural and mechanistic basis remains unknown. Here, we present three crystal structures of full-length dengue virus NS1 complexed with a flavivirus-cross-reactive, NS1-specific monoclonal antibody, 2B7, at resolutions between 2.89 and 3.96 angstroms. These structures reveal a protective mechanism by which two domains of NS1 are antagonized simultaneously. The NS1 wing domain mediates cell binding, whereas the β-ladder triggers downstream events, both of which are required for dengue, Zika, and West Nile virus NS1-mediated endothelial dysfunction. These observations provide a mechanistic explanation for 2B7 protection against NS1-induced pathology and demonstrate the potential of one antibody to treat infections by multiple flaviviruses.


  • Organizational Affiliation
    • Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-3370, USA.

Macromolecule Content 

  • Total Structure Weight: 392.47 kDa 
  • Atom Count: 24,057 
  • Modeled Residue Count: 3,073 
  • Deposited Residue Count: 3,528 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Non-structural protein 1
A, B, C, D
376dengue virus type 1Mutation(s): 0 
UniProt
Find proteins for Q9J7C6 (Dengue virus type 1)
Explore Q9J7C6 
Go to UniProtKB:  Q9J7C6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9J7C6
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
2B7 Fab fragment heavy chain
E, G, I, K
268Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
2B7 Fab fragment light chain
F, H, J, L
238Mus musculusMutation(s): 0 

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
M [auth A]
N [auth A]
O [auth B]
P [auth B]
Q [auth C]
M [auth A],
N [auth A],
O [auth B],
P [auth B],
Q [auth C],
R [auth C],
T [auth D],
U [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
S [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.261 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.446α = 90
b = 329.709β = 90.783
c = 86.717γ = 90
Software Package:
Software NamePurpose
JBluIce-EPICSdata collection
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references, Experimental preparation
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary