6SND

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

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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 of 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LN01 light chainA,
D [auth L]
213Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LN01 heavy chainB,
E [auth H]
235Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160C,
F [auth P]
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
PSF (Subject of Investigation/LOI)
Query on PSF

Download Ideal Coordinates CCD File 
K [auth H]1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE
C18 H34 N O10 P
MIQYPPGTNIFAPO-CABCVRRESA-N
DPV (Subject of Investigation/LOI)
Query on DPV

Download Ideal Coordinates CCD File 
H [auth A]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],
I [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 
J [auth L]PHOSPHOCHOLINE
C5 H15 N O4 P
YHHSONZFOIEMCP-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.707α = 90
b = 137.707β = 90
c = 146.719γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata 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: 2024-11-13
    Changes: Data collection, Database references, Structure summary