Crystal structure of HIV epitope-scaffold 4E10_S0_1Z6NA_001

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 

Starting Model: experimental
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Computational Design of Epitope-Scaffolds Allows Induction of Antibodies Specific for a Poorly Immunogenic HIV Vaccine Epitope.

Correia, B.E.Ban, Y.E.Holmes, M.A.Xu, H.Ellingson, K.Kraft, Z.Carrico, C.Boni, E.Sather, D.N.Zenobia, C.Burke, K.Y.Bradley-Hewitt, T.Bruhn-Johannsen, J.F.Kalyuzhniy, O.Baker, D.Strong, R.K.Stamatatos, L.Schief, W.R.

(2010) Structure 18: 1116-1126

  • DOI: https://doi.org/10.1016/j.str.2010.06.010
  • Primary Citation of Related Structures:  
    3LEF, 3LF6, 3LF9, 3LG7, 3LH2, 3LHP

  • PubMed Abstract: 

    Broadly cross-reactive monoclonal antibodies define epitopes for vaccine development against HIV and other highly mutable viruses. Crystal structures are available for several such antibody-epitope complexes, but methods are needed to translate that structural information into immunogens that re-elicit similar antibodies. We describe a general computational method to design epitope-scaffolds in which contiguous structural epitopes are transplanted to scaffold proteins for conformational stabilization and immune presentation. Epitope-scaffolds designed for the poorly immunogenic but conserved HIV epitope 4E10 exhibited high epitope structural mimicry, bound with higher affinities to monoclonal antibody (mAb) 4E10 than the cognate peptide, and inhibited HIV neutralization by HIV+ sera. Rabbit immunization with an epitope-scaffold induced antibodies with structural specificity highly similar to mAb 4E10, an important advance toward elicitation of neutralizing activity. The results demonstrate that computationally designed epitope-scaffolds are valuable as structure-specific serological reagents and as immunogens to elicit antibodies with predetermined structural specificity.

  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein 4E10_S0_1Z6NA_001 (T18)172synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A]1,2-ETHANEDIOL
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.41α = 90
b = 56.41β = 90
c = 324.13γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2010-09-22 
  • Deposition Author(s): Holmes, M.A.

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description