8EJG | pdb_00008ejg

Structure of lineage VII Lassa virus glycoprotein complex (strain Togo/2016/7082)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8EJG

This is version 1.2 of the entry. See complete history

Literature

Structural conservation of Lassa virus glycoproteins and recognition by neutralizing antibodies.

Perrett, H.R.Brouwer, P.J.M.Hurtado, J.Newby, M.L.Liu, L.Muller-Krauter, H.Muller Aguirre, S.Burger, J.A.Bouhuijs, J.H.Gibson, G.Messmer, T.Schieffelin, J.S.Antanasijevic, A.Boons, G.J.Strecker, T.Crispin, M.Sanders, R.W.Briney, B.Ward, A.B.

(2023) Cell Rep 42: 112524-112524

  • DOI: https://doi.org/10.1016/j.celrep.2023.112524
  • Primary Citation Related Structures: 
    8EJD, 8EJE, 8EJF, 8EJG, 8EJH, 8EJI, 8EJJ

  • PubMed Abstract: 

    Lassa fever is an acute hemorrhagic fever caused by the zoonotic Lassa virus (LASV). The LASV glycoprotein complex (GPC) mediates viral entry and is the sole target for neutralizing antibodies. Immunogen design is complicated by the metastable nature of recombinant GPCs and the antigenic differences among phylogenetically distinct LASV lineages. Despite the sequence diversity of the GPC, structures of most lineages are lacking. We present the development and characterization of prefusion-stabilized, trimeric GPCs of LASV lineages II, V, and VII, revealing structural conservation despite sequence diversity. High-resolution structures and biophysical characterization of the GPC in complex with GP1-A-specific antibodies suggest their neutralization mechanisms. Finally, we present the isolation and characterization of a trimer-preferring neutralizing antibody belonging to the GPC-B competition group with an epitope that spans adjacent protomers and includes the fusion peptide. Our work provides molecular detail information on LASV antigenic diversity and will guide efforts to design pan-LASV vaccines.


  • Organizational Affiliation
    • Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 143.67 kDa 
  • Atom Count: 9,966 
  • Modeled Residue Count: 1,083 
  • Deposited Residue Count: 1,083 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycoprotein GP1A,
C [auth B],
D [auth C]
196Mammarenavirus lassaenseMutation(s): 1 
Gene Names: GPC
UniProt
Find proteins for A0A142I7X5 (Mammarenavirus lassaense)
Explore A0A142I7X5 
Go to UniProtKB:  A0A142I7X5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A142I7X5
Glycosylation
Glycosylation Sites: 7
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycoprotein GP2B [auth a],
E [auth b],
F [auth c]
165Mammarenavirus lassaenseMutation(s): 2 
Gene Names: GPC
UniProt
Find proteins for A0A142I7X5 (Mammarenavirus lassaense)
Explore A0A142I7X5 
Go to UniProtKB:  A0A142I7X5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A142I7X5
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth D],
P [auth M],
W [auth T]
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth F],
R [auth O],
Y [auth V]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth G],
S [auth P],
Z [auth W]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G33431MT
GlyCosmos: G33431MT
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseDA [auth d],
FA [auth f],
N [auth K]
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G07617FP
GlyCosmos: G07617FP
GlyGen: G07617FP

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosetta
RECONSTRUCTIONcryoSPARC3.2

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesINV-004923
Bill & Melinda Gates FoundationUnited StatesOPP1170236

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary