5I8E | pdb_00005i8e

Crystal Structure of Broadly Neutralizing HIV-1 Fusion Peptide-Targeting Antibody VRC34.01 Fab

• PDB DOI: https://doi.org/10.2210/pdb5I8E/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2016-02-18 Released: 2016-05-25 
• Deposition Author(s): Xu, K., Zhou, T., Liu, K., Kwong, P.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.248 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Fusion peptide of HIV-1 as a site of vulnerability to neutralizing antibody.

Kong, R., Xu, K., Zhou, T., Acharya, P., Lemmin, T., Liu, K., Ozorowski, G., Soto, C., Taft, J.D., Bailer, R.T., Cale, E.M., Chen, L., Choi, C.W., Chuang, G.Y., Doria-Rose, N.A., Druz, A., Georgiev, I.S., Gorman, J., Huang, J., Joyce, M.G., Louder, M.K., Ma, X., McKee, K., O'Dell, S., Pancera, M., Yang, Y., Blanchard, S.C., Mothes, W., Burton, D.R., Koff, W.C., Connors, M., Ward, A.B., Kwong, P.D., Mascola, J.R.

(2016) Science 352: 828-833

• PubMed: 27174988 
• DOI: https://doi.org/10.1126/science.aae0474
• Primary Citation Related Structures: 
  5I8C, 5I8E, 5I8H


• PubMed Abstract: 
  

  The HIV-1 fusion peptide, comprising 15 to 20 hydrophobic residues at the N terminus of the Env-gp41 subunit, is a critical component of the virus-cell entry machinery. Here, we report the identification of a neutralizing antibody, N123-VRC34.01, which targets the fusion peptide and blocks viral entry by inhibiting conformational changes in gp120 and gp41 subunits of Env required for entry. Crystal structures of N123-VRC34.01 liganded to the fusion peptide, and to the full Env trimer, revealed an epitope consisting of the N-terminal eight residues of the gp41 fusion peptide and glycan N88 of gp120, and molecular dynamics showed that the N-terminal portion of the fusion peptide can be solvent-exposed. These results reveal the fusion peptide to be a neutralizing antibody epitope and thus a target for vaccine design.

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Organizational Affiliation: 
• Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.
HIV-Specific Immunity Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA.
Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY 10021, USA.
Department of Immunology and Microbial Science, International AIDS Vaccine Initiative Neutralizing Antibody Center, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA 02142, USA.
International AIDS Vaccine Initiative, New York, NY 10038, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 93.75 kDa 
• Atom Count: 6,546 
• Modeled Residue Count: 846 
• Deposited Residue Count: 864 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC34.01 Fab heavy chain	A, C	222	Homo sapiens	Mutation(s): 0  Gene Names: IGHG1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC34.01 Fab light chain	B, D	210	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth C], K [auth C], L [auth C], M [auth C], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.248 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.606	α = 90
b = 114.606	β = 90
c = 174.082	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-05-25 
Deposition Author(s): Xu, K., Zhou, T., Liu, K., Kwong, P.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2016-05-25
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary