6CDO

Structure of vaccine-elicited HIV-1 neutralizing antibody vFP16.02 in complex with HIV-1 fusion peptide residue 512-519


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.226 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SO4Click on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1.

Xu, K.Acharya, P.Kong, R.Cheng, C.Chuang, G.Y.Liu, K.Louder, M.K.O'Dell, S.Rawi, R.Sastry, M.Shen, C.H.Zhang, B.Zhou, T.Asokan, M.Bailer, R.T.Chambers, M.Chen, X.Choi, C.W.Dandey, V.P.Doria-Rose, N.A.Druz, A.Eng, E.T.Farney, S.K.Foulds, K.E.Geng, H.Georgiev, I.S.Gorman, J.Hill, K.R.Jafari, A.J.Kwon, Y.D.Lai, Y.T.Lemmin, T.McKee, K.Ohr, T.Y.Ou, L.Peng, D.Rowshan, A.P.Sheng, Z.Todd, J.P.Tsybovsky, Y.Viox, E.G.Wang, Y.Wei, H.Yang, Y.Zhou, A.F.Chen, R.Yang, L.Scorpio, D.G.McDermott, A.B.Shapiro, L.Carragher, B.Potter, C.S.Mascola, J.R.Kwong, P.D.

(2018) Nat Med 24: 857-867

  • DOI: https://doi.org/10.1038/s41591-018-0042-6
  • Primary Citation of Related Structures:  
    5TKJ, 5TKK, 6CDE, 6CDI, 6CDM, 6CDO, 6CDP

  • PubMed Abstract: 

    A central goal of HIV-1 vaccine research is the elicitation of antibodies capable of neutralizing diverse primary isolates of HIV-1. Here we show that focusing the immune response to exposed N-terminal residues of the fusion peptide, a critical component of the viral entry machinery and the epitope of antibodies elicited by HIV-1 infection, through immunization with fusion peptide-coupled carriers and prefusion stabilized envelope trimers, induces cross-clade neutralizing responses. In mice, these immunogens elicited monoclonal antibodies capable of neutralizing up to 31% of a cross-clade panel of 208 HIV-1 strains. Crystal and cryoelectron microscopy structures of these antibodies revealed fusion peptide conformational diversity as a molecular explanation for the cross-clade neutralization. Immunization of guinea pigs and rhesus macaques induced similarly broad fusion peptide-directed neutralizing responses, suggesting translatability. The N terminus of the HIV-1 fusion peptide is thus a promising target of vaccine efforts aimed at eliciting broadly neutralizing antibodies.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
vFP16.02 Fab heavy chain230Mus musculusMutation(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
vFP16.02 Fab light chain219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 fusion peptide 512-5198Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus type 1)
Explore Q2N0S5 
Go to UniProtKB:  Q2N0S5
Entity Groups  
UniProt GroupQ2N0S5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.226 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.027α = 90
b = 141.027β = 90
c = 77.638γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SO4Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.2: 2024-12-25
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary