+Open data
-Basic information
Entry | Database: PDB / ID: 6p6f | |||||||||||||||
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Title | BG505 SOSIP-I53-50NP | |||||||||||||||
Components |
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Keywords | IMMUNOGEN / 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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / 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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||||||||
Authors | Berndsen, Z.T. / Ward, A.B. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6p6f.cif.gz | 89.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p6f.ent.gz | 63.6 KB | Display | PDB format |
PDBx/mmJSON format | 6p6f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p6f_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6p6f_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6p6f_validation.xml.gz | 39.3 KB | Display | |
Data in CIF | 6p6f_validation.cif.gz | 55.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/6p6f ftp://data.pdbj.org/pub/pdb/validation_reports/p6/6p6f | HTTPS FTP |
-Related structure data
Related structure data | 20261MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | 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 |
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#2: Protein | 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) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Details: unspecified | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average 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 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3590 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT |