5TKJ

Structure of vaccine-elicited diverse HIV-1 neutralizing antibody vFP1.01 in complex with HIV-1 fusion peptide residue 512-519


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.118 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


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:  

  • 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 Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.,National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. jmascola@nih.gov.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. pdkwong@nih.gov.,Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. pdkwong@nih.gov.,Department of Systems Biology, Columbia University, New York, NY, USA.,Vanderbilt Vaccine Center, Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, and Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, USA.,GenScript USA, Piscataway, NJ, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
vFP1.01 chimeric mouse antibody heavy chain
A, D, G, J
221N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
vFP1.01 chimeric mouse antibody light chain
B, E, H, K
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HIV-1 fusion peptide residue 512-519
C, F, I, L
8Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 0 
Gene Names: env
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04578
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, D, G, J
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.118 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.159α = 90.00
b = 120.182β = 90.00
c = 226.182γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
SERGUIdata collection
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2018-06-27
    Type: Data collection, Database references