5UEL

Crystal structure of 354NC102 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Coexistence of potent HIV-1 broadly neutralizing antibodies and antibody-sensitive viruses in a viremic controller.

Freund, N.T.Wang, H.Scharf, L.Nogueira, L.Horwitz, J.A.Bar-On, Y.Golijanin, J.Sievers, S.A.Sok, D.Cai, H.Cesar Lorenzi, J.C.Halper-Stromberg, A.Toth, I.Piechocka-Trocha, A.Gristick, H.B.van Gils, M.J.Sanders, R.W.Wang, L.X.Seaman, M.S.Burton, D.R.Gazumyan, A.Walker, B.D.West, A.P.Bjorkman, P.J.Nussenzweig, M.C.

(2017) Sci Transl Med 9: --

  • DOI: 10.1126/scitranslmed.aal2144
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Some HIV-1-infected patients develop broad and potent HIV-1 neutralizing antibodies (bNAbs) that when passively transferred to mice or macaques can treat or prevent infection. However, bNAbs typically fail to neutralize coexisting autologous viruses ...

    Some HIV-1-infected patients develop broad and potent HIV-1 neutralizing antibodies (bNAbs) that when passively transferred to mice or macaques can treat or prevent infection. However, bNAbs typically fail to neutralize coexisting autologous viruses due to antibody-mediated selection against sensitive viral strains. We describe an HIV-1 controller expressing HLA-B57*01 and HLA-B27*05 who maintained low viral loads for 30 years after infection and developed broad and potent serologic activity against HIV-1. Neutralization was attributed to three different bNAbs targeting nonoverlapping sites on the HIV-1 envelope trimer (Env). One of the three, BG18, an antibody directed against the glycan-V3 portion of Env, is the most potent member of this class reported to date and, as revealed by crystallography and electron microscopy, recognizes HIV-1 Env in a manner that is distinct from other bNAbs in this class. Single-genome sequencing of HIV-1 from serum samples obtained over a period of 9 years showed a diverse group of circulating viruses, 88.5% (31 of 35) of which remained sensitive to at least one of the temporally coincident autologous bNAbs and the individual's serum. Thus, bNAb-sensitive strains of HIV-1 coexist with potent neutralizing antibodies that target the virus and may contribute to control in this individual. When administered as a mix, the three bNAbs controlled viremia in HIV-1 YU2 -infected humanized mice. Our finding suggests that combinations of bNAbs may contribute to control of HIV-1 infection.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742, USA.,Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02129, USA.,Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA. nussen@rockefeller.edu.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA.,Department of Immunology and Microbial Science, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, and International AIDS Vaccine Initiative Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
354NC102 Fab Heavy Chain
H
232N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
354NC102 Fab Light Chain
L
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
H, L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.218α = 90.00
b = 82.499β = 90.00
c = 117.211γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesPJB.HIVRAD-1-NIHP.AL100148

Revision History 

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence
  • Version 1.2: 2017-11-22
    Type: Refinement description