6SND

crystal structure of LN01 Fab in complex with an HIV-1 gp41 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural Basis for Broad HIV-1 Neutralization by the MPER-Specific Human Broadly Neutralizing Antibody LN01.

Pinto, D.Fenwick, C.Caillat, C.Silacci, C.Guseva, S.Dehez, F.Chipot, C.Barbieri, S.Minola, A.Jarrossay, D.Tomaras, G.D.Shen, X.Riva, A.Tarkowski, M.Schwartz, O.Bruel, T.Dufloo, J.Seaman, M.S.Montefiori, D.C.Lanzavecchia, A.Corti, D.Pantaleo, G.Weissenhorn, W.

(2019) Cell Host Microbe --: --

  • DOI: 10.1016/j.chom.2019.09.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Potent and broadly neutralizing antibodies (bnAbs) are the hallmark of HIV-1 protection by vaccination. The membrane-proximal external region (MPER) of the HIV-1 gp41 fusion protein is targeted by the most broadly reactive HIV-1 neutralizing antibodi ...

    Potent and broadly neutralizing antibodies (bnAbs) are the hallmark of HIV-1 protection by vaccination. The membrane-proximal external region (MPER) of the HIV-1 gp41 fusion protein is targeted by the most broadly reactive HIV-1 neutralizing antibodies. Here, we examine the structural and molecular mechansims of neutralization by anti-MPER bnAb, LN01, which was isolated from lymph-node-derived germinal center B cells of an elite controller and exhibits broad neutralization breadth. LN01 engages both MPER and the transmembrane (TM) region, which together form a continuous helix in complex with LN01. The tilted TM orientation allows LN01 to interact simultaneously with the peptidic component of the MPER epitope and membrane via two specific lipid binding sites of the antibody paratope. Although LN01 carries a high load of somatic mutations, most key residues interacting with the MPER epitope and lipids are germline encoded, lending support for the LN01 epitope as a candidate for lineage-based vaccine development.


    Organizational Affiliation

    Institut Pasteur, Virus & Immunity Unit, CNRS UMR 3569, Paris 75015, France; Vaccine Research Institute, 94000 Créteil, France.,Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France.,Swiss Vaccine Research Institute, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland. Electronic address: giuseppe.pantaleo@chuv.ch.,Duke Human Vaccine Institute, Durham, NC 27710, USA; Paris Diderot University, Sorbonne Paris Cité, Paris 75013, France.,Humabs Biomed SA, Vir Biotechnology, 6500 Bellinzona, Ticino, Switzerland. Electronic address: dcorti@vir.bio.,Duke Human Vaccine Institute, Durham, NC 27710, USA.,LPCT, UMR 7019 Université de Lorraine CNRS, 54500 Vandœuvre-lès-Nancy, France; Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, LPCT, UMR 7019 Universiteé de Lorraine CNRS, Vandœuvre-lès-Nancy 54500, France; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,LPCT, UMR 7019 Université de Lorraine CNRS, 54500 Vandœuvre-lès-Nancy, France; Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, LPCT, UMR 7019 Universiteé de Lorraine CNRS, Vandœuvre-lès-Nancy 54500, France.,Swiss Vaccine Research Institute, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland.,Department of Biomedical and Clinical Sciences, Luigi Sacco University Hospital, Università di Milano, 20157 Milan, Italy; III Division of Infectious Diseases, ASST Fatebenefratelli-Sacco, 20157 Milan, Italy.,Department of Biomedical and Clinical Sciences, Luigi Sacco University Hospital, Università di Milano, 20157 Milan, Italy.,Institute for Research in Biomedicine, Bellinzona 6500, Ticino, Switzerland.,Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.,Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA.,Humabs Biomed SA, Vir Biotechnology, 6500 Bellinzona, Ticino, Switzerland.,Institut Pasteur, Virus & Immunity Unit, CNRS UMR 3569, Paris 75015, France; Vaccine Research Institute, 94000 Créteil, France; Paris Diderot University, Sorbonne Paris Cité, Paris 75013, France.,Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France. Electronic address: winfried.weissenhorn@ibs.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LN01 light chain
A, L
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LN01 heavy chain
B, H
235N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
C, P
25Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for G3DH64 (Human immunodeficiency virus 1)
Go to UniProtKB:  G3DH64
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PC
Query on PC

Download SDF File 
Download CCD File 
L
PHOSPHOCHOLINE
C5 H15 N O4 P
YHHSONZFOIEMCP-UHFFFAOYSA-O
 Ligand Interaction
PSF
Query on PSF

Download SDF File 
Download CCD File 
H
1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE
PHOSPHATIDYLSERINE
C18 H34 N O10 P
MIQYPPGTNIFAPO-CABCVRRESA-N
 Ligand Interaction
DPV
Query on DPV

Download SDF File 
Download CCD File 
A
dodecyl 2-(trimethylammonio)ethyl phosphate
dodecylphosphocholine
C17 H38 N O4 P
QBHFVMDLPTZDOI-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, L
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.238 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 137.707α = 90.00
b = 137.707β = 90.00
c = 146.719γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHENIXphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationSwitzerlandOPP1114725
Bill & Melinda Gates FoundationSwitzerlandOPP1032144
European CommissionFranceNo. 681137, H2020 EAVI

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release