6MTT

Crystal structure of VRC46.01 Fab in complex with gp41 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Longitudinal Analysis Reveals Early Development of Three MPER-Directed Neutralizing Antibody Lineages from an HIV-1-Infected Individual.

Krebs, S.J.Kwon, Y.D.Schramm, C.A.Law, W.H.Donofrio, G.Zhou, K.H.Gift, S.Dussupt, V.Georgiev, I.S.Schatzle, S.McDaniel, J.R.Lai, Y.T.Sastry, M.Zhang, B.Jarosinski, M.C.Ransier, A.Chenine, A.L.Asokan, M.Bailer, R.T.Bose, M.Cagigi, A.Cale, E.M.Chuang, G.Y.Darko, S.Driscoll, J.I.Druz, A.Gorman, J.Laboune, F.Louder, M.K.McKee, K.Mendez, L.Moody, M.A.O'Sullivan, A.M.Owen, C.Peng, D.Rawi, R.Sanders-Buell, E.Shen, C.H.Shiakolas, A.R.Stephens, T.Tsybovsky, Y.Tucker, C.Verardi, R.Wang, K.Zhou, J.Zhou, T.Georgiou, G.Alam, S.M.Haynes, B.F.Rolland, M.Matyas, G.R.Polonis, V.R.McDermott, A.B.Douek, D.C.Shapiro, L.Tovanabutra, S.Michael, N.L.Mascola, J.R.Robb, M.L.Kwong, P.D.Doria-Rose, N.A.

(2019) Immunity 50: 677-691.e13

  • DOI: 10.1016/j.immuni.2019.02.008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lineage-based vaccine design is an attractive approach for eliciting broadly neutralizing antibodies (bNAbs) against HIV-1. However, most bNAb lineages studied to date have features indicative of unusual recombination and/or development. From an indi ...

    Lineage-based vaccine design is an attractive approach for eliciting broadly neutralizing antibodies (bNAbs) against HIV-1. However, most bNAb lineages studied to date have features indicative of unusual recombination and/or development. From an individual in the prospective RV217 cohort, we identified three lineages of bNAbs targeting the membrane-proximal external region (MPER) of the HIV-1 envelope. Antibodies RV217-VRC42.01, -VRC43.01, and -VRC46.01 used distinct modes of recognition and neutralized 96%, 62%, and 30%, respectively, of a 208-strain virus panel. All three lineages had modest levels of somatic hypermutation and normal antibody-loop lengths and were initiated by the founder virus MPER. The broadest lineage, VRC42, was similar to the known bNAb 4E10. A multimeric immunogen based on the founder MPER activated B cells bearing the unmutated common ancestor of VRC42, with modest maturation of early VRC42 intermediates imparting neutralization breadth. These features suggest that VRC42 may be a promising template for lineage-based vaccine design.


    Organizational Affiliation

    Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA.,U.S. Military HIV Research Program, WRAIR, Silver Spring, MD, USA.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; Columbia University, New York, NY, USA. Electronic address: pdkwong@nih.gov.,U.S. Military HIV Research Program, WRAIR, Silver Spring, MD, USA; Henry Jackson Foundation, Bethesda, MD, USA.,Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. Electronic address: nicole.doriarose@nih.gov.,Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.,Duke University School of Medicine and Center for HIV/AIDS Vaccine Immunology - Immunogen Discovery, Durham, NC, USA.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; 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
Antibody VRC46.01 Fb light chain
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antibody VRC46.01 Fab heavy chain
H
224N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RV217 founder virus gp41 peptide
P
28Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for A7L302 (Human immunodeficiency virus 1)
Go to UniProtKB:  A7L302
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.235 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 124.602α = 90.00
b = 49.162β = 97.10
c = 99.967γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (United States)United StatesW-31-109-Eng-38

Revision History 

  • Version 1.0: 2019-03-27
    Type: Initial release