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- PDB-6p6f: BG505 SOSIP-I53-50NP -

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Basic information

Entry
Database: PDB / ID: 6p6f
TitleBG505 SOSIP-I53-50NP
Components
  • I53-50A.1NT1
  • I53-50B.4PT1
KeywordsIMMUNOGEN / nanoparticle / self-assembling / HIV / SOSIP
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsBerndsen, Z.T. / Ward, A.B.
Funding support United States, 4items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1111923 United States
Bill & Melinda Gates FoundationOPP1132237 United States
Bill & Melinda Gates FoundationOPP1115782 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI110657 United States
CitationJournal: Nat Commun / Year: 2019
Title: Enhancing and shaping the immunogenicity of native-like HIV-1 envelope trimers with a two-component protein nanoparticle.
Authors: Philip J M Brouwer / Aleksandar Antanasijevic / Zachary Berndsen / Anila Yasmeen / Brooke Fiala / Tom P L Bijl / Ilja Bontjer / Jacob B Bale / William Sheffler / Joel D Allen / Anna Schorcht ...Authors: Philip J M Brouwer / Aleksandar Antanasijevic / Zachary Berndsen / Anila Yasmeen / Brooke Fiala / Tom P L Bijl / Ilja Bontjer / Jacob B Bale / William Sheffler / Joel D Allen / Anna Schorcht / Judith A Burger / Miguel Camacho / Daniel Ellis / Christopher A Cottrell / Anna-Janina Behrens / Marco Catalano / Iván Del Moral-Sánchez / Thomas J Ketas / Celia LaBranche / Marit J van Gils / Kwinten Sliepen / Lance J Stewart / Max Crispin / David C Montefiori / David Baker / John P Moore / Per Johan Klasse / Andrew B Ward / Neil P King / Rogier W Sanders /
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. ...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.
History
DepositionJun 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Structure summary / Category: struct_keywords
Item: _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-20261
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  • Superimposition on EM map
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: I53-50A.1NT1
B: I53-50B.4PT1


Theoretical massNumber of molelcules
Total (without water)117,6242
Polymers117,6242
Non-polymers00
Water0
1
A: I53-50A.1NT1
B: I53-50B.4PT1
x 60


Theoretical massNumber of molelcules
Total (without water)7,057,415120
Polymers7,057,415120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: I53-50A.1NT1
B: I53-50B.4PT1
x 5


  • icosahedral pentamer
  • 588 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)588,11810
Polymers588,11810
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: I53-50A.1NT1
B: I53-50B.4PT1
x 6


  • icosahedral 23 hexamer
  • 706 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)705,74212
Polymers705,74212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein I53-50A.1NT1


Mass: 99386.711 Da / Num. of mol.: 1 / Fragment: fusion of BG505 SOSIP.664 + GSG linker + I53-50A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6*PLUS
#2: Protein I53-50B.4PT1


Mass: 18236.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Two-component self-assembling nanoparticle consisting of BG505 SOSIP-I53-50A.1NT1 and I53-50B.4PT1COMPLEXall0MULTIPLE SOURCES
2I53-50A.1NT1COMPLEX#11RECOMBINANT
3I53-50B.4PT1COMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12synthetic construct (others)32630
23synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
12Homo sapiens (human)9606HEK293F
23Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)1182032
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 8 sec. / Electron dose: 10 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategory
2Leginonimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
12RELION23D reconstruction
13Rosettamodel refinement
14PHENIXmodel refinement
15Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3590 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT

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