8U03

Crystal structure of non-glycosylated 10E8-GT10.1 scaffold in complex with a human 10E8 NGS precursor (10E8-NGS-03)

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2023-08-28 Released: 2024-06-12 
  • Deposition Author(s): Irimia, A., Wilson, I.A.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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
10E8-NGS-03 Fab heavy chainA [auth H]232Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
10E8-NGS-03 Fab Light ChainB [auth L]211Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
10E8-GT10.1 epitope scaffold155Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
D [auth L]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
E [auth L]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.599α = 90
b = 85.218β = 90
c = 175.432γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI144462
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI147826

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-12
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Structure summary