6P95

Structure of Lassa virus glycoprotein in complex with Fab 25.6A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Convergent Structures Illuminate Features for Germline Antibody Binding and Pan-Lassa Virus Neutralization.

Hastie, K.M.Cross, R.W.Harkins, S.S.Zandonatti, M.A.Koval, A.P.Heinrich, M.L.Rowland, M.M.Robinson, J.E.Geisbert, T.W.Garry, R.F.Branco, L.M.Saphire, E.O.

(2019) Cell 178: 1004-1015.e14

  • DOI: 10.1016/j.cell.2019.07.020
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lassa virus (LASV) causes hemorrhagic fever and is endemic in West Africa. Protective antibody responses primarily target the LASV surface glycoprotein (GPC), and GPC-B competition group antibodies often show potent neutralizing activity in humans. H ...

    Lassa virus (LASV) causes hemorrhagic fever and is endemic in West Africa. Protective antibody responses primarily target the LASV surface glycoprotein (GPC), and GPC-B competition group antibodies often show potent neutralizing activity in humans. However, which features confer potent and broadly neutralizing antibody responses is unclear. Here, we compared three crystal structures of LASV GPC complexed with GPC-B antibodies of varying neutralization potency. Each GPC-B antibody recognized an overlapping epitope involved in binding of two adjacent GPC monomers and preserved the prefusion trimeric conformation. Differences among GPC-antibody interactions highlighted specific residues that enhance neutralization. Using structure-guided amino acid substitutions, we increased the neutralization potency and breadth of these antibodies to include all major LASV lineages. The ability to define antibody residues that allow potent and broad neutralizing activity, together with findings from analyses of inferred germline precursors, is critical to develop potent therapeutics and for vaccine design and assessment.


    Organizational Affiliation

    La Jolla Institute for Immunology, La Jolla, CA, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,La Jolla Institute for Immunology, La Jolla, CA, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA. Electronic address: erica@lji.org.,Department of Pediatrics, School of Medicine, Tulane University, New Orleans, LA, USA.,University of Texas Medical Branch, Galveston National Laboratory, Galveston, TX, USA.,Zalgen Labs, Germantown, MD, USA.,Zalgen Labs, Germantown, MD, USA; Department of Microbiology and Immunology, Tulane University, New Orleans, LA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pre-glycoprotein polyprotein GP complex
A, B, C
259Lassa virus (strain Mouse/Sierra Leone/Josiah/1976)Mutation(s): 3 
Gene Names: GPC (GP-C)
Find proteins for P08669 (Lassa virus (strain Mouse/Sierra Leone/Josiah/1976))
Go to UniProtKB:  P08669
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FAB Antibody heavy chain
D, F, H
231N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FAB Antibody light chain
E, G, L
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Pre-glycoprotein polyprotein GP complex
a, b, c
180Lassa virus (strain Mouse/Sierra Leone/Josiah/1976)Mutation(s): 3 
Gene Names: GPC (GP-C)
Find proteins for P08669 (Lassa virus (strain Mouse/Sierra Leone/Josiah/1976))
Go to UniProtKB:  P08669
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
a, B, b, c
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
a, b, c
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
a, A, b, B, C, c
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, a, b, B, c, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.205 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 152.242α = 90.00
b = 152.242β = 90.00
c = 453.889γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesU19AI109762-05

Revision History 

  • Version 1.0: 2019-09-11
    Type: Initial release