8V2E

Crystal structure of B055 scaffold boost immunogen in complex with a mature 10E8 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Vaccination induces broadly neutralizing antibody precursors to HIV gp41.

Schiffner, T.Phung, I.Ray, R.Irimia, A.Tian, M.Swanson, O.Lee, J.H.Lee, C.D.Marina-Zarate, E.Cho, S.Y.Huang, J.Ozorowski, G.Skog, P.D.Serra, A.M.Rantalainen, K.Allen, J.D.Baboo, S.Rodriguez, O.L.Himansu, S.Zhou, J.Hurtado, J.Flynn, C.T.McKenney, K.Havenar-Daughton, C.Saha, S.Shields, K.Schulze, S.Smith, M.L.Liang, C.H.Toy, L.Pecetta, S.Lin, Y.C.Willis, J.R.Sesterhenn, F.Kulp, D.W.Hu, X.Cottrell, C.A.Zhou, X.Ruiz, J.Wang, X.Nair, U.Kirsch, K.H.Cheng, H.L.Davis, J.Kalyuzhniy, O.Liguori, A.Diedrich, J.K.Ngo, J.T.Lewis, V.Phelps, N.Tingle, R.D.Spencer, S.Georgeson, E.Adachi, Y.Kubitz, M.Eskandarzadeh, S.Elsliger, M.A.Amara, R.R.Landais, E.Briney, B.Burton, D.R.Carnathan, D.G.Silvestri, G.Watson, C.T.Yates 3rd, J.R.Paulson, J.C.Crispin, M.Grigoryan, G.Ward, A.B.Sok, D.Alt, F.W.Wilson, I.A.Batista, F.D.Crotty, S.Schief, W.R.

(2024) Nat Immunol 25: 1073-1082

  • DOI: https://doi.org/10.1038/s41590-024-01833-w
  • Primary Citation of Related Structures:  
    8SX3, 8TZN, 8TZW, 8U03, 8U08, 8V2E

  • PubMed Abstract: 

    A key barrier to the development of vaccines that induce broadly neutralizing antibodies (bnAbs) against human immunodeficiency virus (HIV) and other viruses of high antigenic diversity is the design of priming immunogens that induce rare bnAb-precursor B cells. The high neutralization breadth of the HIV bnAb 10E8 makes elicitation of 10E8-class bnAbs desirable; however, the recessed epitope within gp41 makes envelope trimers poor priming immunogens and requires that 10E8-class bnAbs possess a long heavy chain complementarity determining region 3 (HCDR3) with a specific binding motif. We developed germline-targeting epitope scaffolds with affinity for 10E8-class precursors and engineered nanoparticles for multivalent display. Scaffolds exhibited epitope structural mimicry and bound bnAb-precursor human naive B cells in ex vivo screens, protein nanoparticles induced bnAb-precursor responses in stringent mouse models and rhesus macaques, and mRNA-encoded nanoparticles triggered similar responses in mice. Thus, germline-targeting epitope scaffold nanoparticles can elicit rare bnAb-precursor B cells with predefined binding specificities and HCDR3 features.


  • Organizational Affiliation

    Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody 10E8 FAB HEAVY CHAIN
A, D
234Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody 10E8 FAB LIGHT CHAIN
B, E
215Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
10E8 EPITOPE SCAFFOLD B055
C, F
188synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.032α = 90
b = 84.941β = 90
c = 205.969γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
Cootmodel building
PHENIXrefinement

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--
International AIDS Vaccine InitiativeUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-12
    Type: Initial release