6P6F | pdb_00006p6f

BG505 SOSIP-I53-50NP

• PDB DOI: https://doi.org/10.2210/pdb6P6F/pdb
• EM Map EMD-20261: EMDB EMDataResource

• Classification: IMMUNOGEN
• Organism(s): synthetic construct
• Expression System: Homo sapiens, Escherichia coli-Pichia pastoris shuttle vector pPpARG4
• Mutation(s): No 


• Deposited: 2019-06-03 Released: 2019-06-19 
• Deposition Author(s): Berndsen, Z.T., Ward, A.B.
• Funding Organization(s): Bill & Melinda Gates Foundation, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Enhancing and shaping the immunogenicity of native-like HIV-1 envelope trimers with a two-component protein nanoparticle.

Brouwer, P.J.M., Antanasijevic, A., Berndsen, Z., Yasmeen, A., Fiala, B., Bijl, T.P.L., Bontjer, I., Bale, J.B., Sheffler, W., Allen, J.D., Schorcht, A., Burger, J.A., Camacho, M., Ellis, D., Cottrell, C.A., Behrens, A.J., Catalano, M., Del Moral-Sanchez, I., Ketas, T.J., LaBranche, C., van Gils, M.J., Sliepen, K., Stewart, L.J., Crispin, M., Montefiori, D.C., Baker, D., Moore, J.P., Klasse, P.J., Ward, A.B., King, N.P., Sanders, R.W.

(2019) Nat Commun 10: 4272-4272

• PubMed: 31537780 
• DOI: https://doi.org/10.1038/s41467-019-12080-1
• Primary Citation Related Structures: 
  6P6F


• PubMed Abstract: 
  

  The development of native-like HIV-1 envelope (Env) trimer antigens has enabled the induction of neutralizing antibody (NAb) responses against neutralization-resistant HIV-1 strains in animal models. However, NAb responses are relatively weak and narrow in specificity. Displaying antigens in a multivalent fashion on nanoparticles (NPs) is an established strategy to increase their immunogenicity. Here we present the design and characterization of two-component protein NPs displaying 20 stabilized SOSIP trimers from various HIV-1 strains. The two-component nature permits the incorporation of exclusively well-folded, native-like Env trimers into NPs that self-assemble in vitro with high efficiency. Immunization studies show that the NPs are particularly efficacious as priming immunogens, improve the quality of the Ab response over a conventional one-component nanoparticle system, and are most effective when SOSIP trimers with an apex-proximate neutralizing epitope are displayed. Their ability to enhance and shape the immunogenicity of SOSIP trimers make these NPs a promising immunogen platform.

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Organizational Affiliation: 
• Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA.
Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, 10065, USA.
Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA.
Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA.
Arzeda Corporation, Seattle, Washington, 98119, USA.
Biological Sciences and Institute of Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK.
Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, OX1 3QU, Oxford, UK.
New England Biolabs, Inc., Ipswich, Massachussetts, 01938, USA.
Department of Surgery, Duke University Medical Center, Durham, North Carolina, 27710, USA.
Howard Hughes Medical Institute, University of Washington, Seattle, Washington, 98105, USA.
Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA. [e-mail].
Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA. [e-mail].
Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands. [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)

Biological Assembly Evidence: microscopy, native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 117.62 kDa 
• Atom Count: 2,664 
• Modeled Residue Count: 351 
• Deposited Residue Count: 1,065 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
I53-50A.1NT1	A	898	synthetic construct	Mutation(s): 0
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1) Explore Q2N0S6  Go to UniProtKB:  Q2N0S6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
I53-50B.4PT1	B	167	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2
MODEL REFINEMENT	Rosetta
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-06-19 
Deposition Author(s): Berndsen, Z.T., Ward, A.B.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	OPP1111923
Bill & Melinda Gates Foundation	United States	OPP1132237
Bill & Melinda Gates Foundation	United States	OPP1115782
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 AI110657

Revision History  

• Version 1.0: 2019-06-19
  Type: Initial release
  
• Version 1.1: 2019-09-11
  Changes: Data collection, Structure summary
• Version 1.2: 2019-10-02
  Changes: Data collection, Database references
• Version 1.3: 2019-12-18
  Changes: Author supporting evidence
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary