5AAW

Structure of a redesigned cross-reactive antibody to dengue virus with increased in vivo potency


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-Guided Design of an Anti-Dengue Antibody Directed to a Non-Immunodominant Epitope.

Robinson, L.N.Tharakaraman, K.Rowley, K.J.Costa, V.V.Chan, K.R.Wong, Y.H.Ong, L.C.Tan, H.C.Koch, T.Cain, D.Kirloskar, R.Viswanathan, K.Liew, C.W.Tissire, H.Ramakrishnan, B.Myette, J.R.Babcock, G.J.Sasisekharan, V.Alonso, S.Chen, J.Lescar, J.Shriver, Z.Ooi, E.E.Sasisekharan, R.

(2015) Cell 162: 493

  • DOI: https://doi.org/10.1016/j.cell.2015.06.057
  • Primary Citation of Related Structures:  
    5AAM, 5AAW

  • PubMed Abstract: 

    Dengue is the most common vector-borne viral disease, causing nearly 400 million infections yearly. Currently there are no approved therapies. Antibody epitopes that elicit weak humoral responses may not be accessible by conventional B cell panning methods. To demonstrate an alternative strategy to generating a therapeutic antibody, we employed a non-immunodominant, but functionally relevant, epitope in domain III of the E protein, and engineered by structure-guided methods an antibody directed to it. The resulting antibody, Ab513, exhibits high-affinity binding to, and broadly neutralizes, multiple genotypes within all four serotypes. To assess therapeutic relevance of Ab513, activity against important human clinical features of dengue was investigated. Ab513 mitigates thrombocytopenia in a humanized mouse model, resolves vascular leakage, reduces viremia to nearly undetectable levels, and protects mice in a maternal transfer model of lethal antibody-mediated enhancement. The results demonstrate that Ab513 may reduce the public health burden from dengue.


  • Organizational Affiliation

    Visterra Inc., One Kendall Square, Suite B3301, Cambridge, MA 02139, USA; Department of Biological Engineering, Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge MA 02139; USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SCFV513
A, B, D, F, H
A, B, D, F, H, K
252Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DENGUE SEROTYPE 4 ENVELOPE PROTEIN DOMAIN 3
C, E, G, I, J
C, E, G, I, J, L
115Dengue virusMutation(s): 0 
UniProt
Find proteins for Q6YFR6 (dengue virus type 4)
Explore Q6YFR6 
Go to UniProtKB:  Q6YFR6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6YFR6
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.11α = 90
b = 131.67β = 90
c = 176.45γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2016-04-06
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Other, Refinement description