6CDM

Structure of vaccine-elicited HIV-1 neutralizing antibody vFP7.04 in complex with HIV-1 fusion peptide residue 512-519

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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This is version 1.1 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: 10.1038/s41591-018-0042-6
  • Primary Citation of Related Structures:  
    5TKK, 5TKJ, 6CDP, 6CDO, 6CDI, 6CDM, 6CDE

  • 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 compo ...

    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: 

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. pdkwong@nih.gov.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
vFP7.04 heavy chainA, D221Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
vFP7.04 light chainB, E219Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HIV fusion peptide (512-519)C, F8Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q2N0S5 (Human immunodeficiency virus 1)
Explore Q2N0S5 
Go to UniProtKB:  Q2N0S5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.565α = 90
b = 61.034β = 91.89
c = 88.654γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection, Database references