6SNC | pdb_00006snc

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.254 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6SNC

Ligand Structure Quality Assessment 


This is version 1.3 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 26: 623-637.e8

  • DOI: https://doi.org/10.1016/j.chom.2019.09.016
  • Primary Citation Related Structures: 
    6SNC, 6SND, 6SNE

  • 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 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
    • Institute for Research in Biomedicine, Bellinzona 6500, Ticino, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 105.65 kDa 
  • Atom Count: 7,172 
  • Modeled Residue Count: 914 
  • Deposited Residue Count: 948 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LNO1 Light ChainA,
C [auth L]
214Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
LNO1 Heavy ChainB,
D [auth H]
235Homo sapiensMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160E [auth P],
F [auth C]
25Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04578 
Go to UniProtKB:  P04578
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04578
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DPV
(Subject of Investigation/LOI)

Query on DPV



Download:Ideal Coordinates CCD File
K [auth H]dodecyl 2-(trimethylammonio)ethyl phosphate
C17 H38 N O4 P
QBHFVMDLPTZDOI-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
G [auth A],
J [auth L]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PC
(Subject of Investigation/LOI)

Query on PC



Download:Ideal Coordinates CCD File
L [auth P],
M [auth C]
PHOSPHOCHOLINE
C5 H15 N O4 P
YHHSONZFOIEMCP-UHFFFAOYSA-O
PO4

Query on PO4



Download:Ideal Coordinates CCD File
H [auth B],
I [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.254 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.762α = 90
b = 136.762β = 90
c = 146.908γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Structure summary