8SX3

10E8-GT10.2 immunogen in complex with human Fab 10E8 and mouse Fab W6-10


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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
W6-10 mouse Fab heavy chain224Mus 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
W6-10 mouse light chain214Mus 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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
10E8-GT10.2 immunogen187synthetic constructMutation(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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
10E8 Fab heavy chainD [auth H]234Homo sapiensMutation(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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
10E8 light chainE [auth L]215Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth D]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesINV-002916
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM1 AI144462

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Database references