7SGE | pdb_00007sge

I53-50 nanoparticle core reconstructed from GPC-I53-50NP by focused refinement

• PDB DOI: https://doi.org/10.2210/pdb7SGE/pdb
• EM Map EMD-25108: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): synthetic construct
• Expression System: Homo sapiens, Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2021-10-05 Released: 2022-10-12 
• Deposition Author(s): Antanasijevic, A., Brouwer, P.J.M., Ward, A.B.
• Funding Organization(s): Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.67 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Lassa virus glycoprotein nanoparticles elicit neutralizing antibody responses and protection.

Brouwer, P.J.M., Antanasijevic, A., Ronk, A.J., Muller-Krauter, H., Watanabe, Y., Claireaux, M., Perrett, H.R., Bijl, T.P.L., Grobben, M., Umotoy, J.C., Schriek, A.I., Burger, J.A., Tejjani, K., Lloyd, N.M., Steijaert, T.H., van Haaren, M.M., Sliepen, K., de Taeye, S.W., van Gils, M.J., Crispin, M., Strecker, T., Bukreyev, A., Ward, A.B., Sanders, R.W.

(2022) Cell Host Microbe 30: 1759

• PubMed: 36400021 
• DOI: https://doi.org/10.1016/j.chom.2022.10.018
• Primary Citation Related Structures: 
  7SGD, 7SGE, 7SGF


• PubMed Abstract: 
  

  The Lassa virus is endemic in parts of West Africa, and it causes hemorrhagic fever with high mortality. The development of a recombinant protein vaccine has been hampered by the instability of soluble Lassa virus glycoprotein complex (GPC) trimers, which disassemble into monomeric subunits after expression. Here, we use two-component protein nanoparticles consisting of trimeric and pentameric subunits to stabilize GPC in a trimeric conformation. These GPC nanoparticles present twenty prefusion GPC trimers on the surface of an icosahedral particle. Cryo-EM studies of GPC nanoparticles demonstrated a well-ordered structure and yielded a high-resolution structure of an unliganded GPC. These nanoparticles induced potent humoral immune responses in rabbits and protective immunity against the lethal Lassa virus challenge in guinea pigs. Additionally, we isolated a neutralizing antibody that mapped to the putative receptor-binding site, revealing a previously undefined site of vulnerability. Collectively, these findings offer potential approaches to vaccine and therapeutic design for the Lassa virus.

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Organizational Affiliation: 
• Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands; Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.
Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550, USA; Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77550, USA.
Institute of Virology, Philipps University Marburg, 35043 Marburg, Germany.
School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands.
Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: [e-mail].
Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 120-mer - A60B60 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 92.08 kDa 
• Atom Count: 2,657 
• Modeled Residue Count: 351 
• Deposited Residue Count: 832 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Josiah GPCysR4-I53-50A - nanoparticle component	A	665	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
I53-50B component	B	167	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.67 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	RosettaEM
MODEL REFINEMENT	Coot

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-12 
Deposition Author(s): Antanasijevic, A., Brouwer, P.J.M., Ward, A.B.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	OPP1170236

Revision History  

• Version 1.0: 2022-10-12
  Type: Initial release
  
• Version 1.1: 2022-11-30
  Changes: Database references, Refinement description
• Version 1.2: 2022-12-28
  Changes: Database references
• Version 1.3: 2024-10-16
  Changes: Data collection, Refinement description, Structure summary