8TDX

TRNM-b.01 in complex with HIV Env fusion peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Potent and broad HIV-1 neutralization in fusion peptide-primed SHIV-infected macaques.

Wang, H.Cheng, C.Dal Santo, J.L.Shen, C.H.Bylund, T.Henry, A.R.Howe, C.A.Hwang, J.Morano, N.C.Morris, D.J.Pletnev, S.Roark, R.S.Zhou, T.Hansen, B.T.Hoyt, F.H.Johnston, T.S.Wang, S.Zhang, B.Ambrozak, D.R.Becker, J.E.Bender, M.F.Changela, A.Chaudhary, R.Corcoran, M.Corrigan, A.R.Foulds, K.E.Guo, Y.Lee, M.Li, Y.Lin, B.C.Liu, T.Louder, M.K.Mandolesi, M.Mason, R.D.McKee, K.Nair, V.O'Dell, S.Olia, A.S.Ou, L.Pegu, A.Raju, N.Rawi, R.Roberts-Torres, J.Sarfo, E.K.Sastry, M.Schaub, A.J.Schmidt, S.D.Schramm, C.A.Schwartz, C.L.Smith, S.C.Stephens, T.Stuckey, J.Teng, I.T.Todd, J.P.Tsybovsky, Y.Van Wazer, D.J.Wang, S.Doria-Rose, N.A.Fischer, E.R.Georgiev, I.S.Karlsson Hedestam, G.B.Sheng, Z.Woodward, R.A.Douek, D.C.Koup, R.A.Pierson, T.C.Shapiro, L.Shaw, G.M.Mascola, J.R.Kwong, P.D.

(2024) Cell 

  • DOI: https://doi.org/10.1016/j.cell.2024.10.003
  • Primary Citation of Related Structures:  
    8TDX, 8TE7, 8TNU, 8TO7, 8TO9

  • PubMed Abstract: 

    An antibody-based HIV-1 vaccine will require the induction of potent cross-reactive HIV-1-neutralizing responses. To demonstrate feasibility toward this goal, we combined vaccination targeting the fusion-peptide site of vulnerability with infection by simian-human immunodeficiency virus (SHIV). In four macaques with vaccine-induced neutralizing responses, SHIV infection boosted plasma neutralization to 45%-77% breadth (geometric mean 50% inhibitory dilution [ID 50 ] ∼100) on a 208-strain panel. Molecular dissection of these responses by antibody isolation and cryo-electron microscopy (cryo-EM) structure determination revealed 15 of 16 antibody lineages with cross-clade neutralization to be directed toward the fusion-peptide site of vulnerability. In each macaque, isolated antibodies from memory B cells recapitulated the plasma-neutralizing response, with fusion-peptide-binding antibodies reaching breadths of 40%-60% (50% inhibitory concentration [IC 50 ] < 50 μg/mL) and total lineage-concentrations estimates of 50-200 μg/mL. Longitudinal mapping indicated that these responses arose prior to SHIV infection. Collectively, these results provide in vivo molecular examples for one to a few B cell lineages affording potent, broadly neutralizing plasma responses.


  • Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRNM-b.01 Fab Heavy ChainA,
D [auth B]
227Macaca mulattaMutation(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
TRNM-b.01 Fab Light ChainB [auth C],
C [auth D]
213Macaca mulattaMutation(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
Env Fusion PeptideE [auth F],
F [auth E]
8Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for P12489 (Human immunodeficiency virus type 1 group M subtype B (isolate JH32))
Explore P12489 
Go to UniProtKB:  P12489
Entity Groups  
UniProt GroupP12489
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.464α = 90
b = 88.926β = 90
c = 129.108γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SERGUIdata collection
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Database references, Structure summary