6CDM | pdb_00006cdm

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

• PDB DOI: https://doi.org/10.2210/pdb6CDM/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Human immunodeficiency virus 1
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2018-02-08 Released: 2018-05-16 
• Deposition Author(s): Xu, K., Liu, K., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

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

• PubMed: 29867235 
• DOI: https://doi.org/10.1038/s41591-018-0042-6
• Primary Citation 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.

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Organizational Affiliation: 
• Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 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.
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
Department of Systems Biology, Columbia University, New York, NY, USA.
Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
GenScript USA, Piscataway, NJ, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. [e-mail].
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. [e-mail].
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 96.97 kDa 
• Atom Count: 7,075 
• Modeled Residue Count: 884 
• Deposited Residue Count: 896 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
vFP7.04 heavy chain	A, D	221	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
vFP7.04 light chain	B, E	219	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV fusion peptide (512-519)	C, F	8	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus type 1) Explore Q2N0S5  Go to UniProtKB:  Q2N0S5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.565	α = 90
b = 61.034	β = 91.89
c = 88.654	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-16 
Deposition Author(s): Xu, K., Liu, K., Kwong, P.D.

Revision History  

• Version 1.0: 2018-05-16
  Type: Initial release
  
• Version 1.1: 2018-06-20
  Changes: Data collection, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary