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- PDB-8ur7: I53_dn5 nanoparticle displaying the trimeric HA heads with heptad... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ur7 | ||||||
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Title | I53_dn5 nanoparticle displaying the trimeric HA heads with heptad domain, TH-6heptad-I53_dn5 (local refinement of TH-6heptad) | ||||||
![]() | Trimer head HA,Hemagglutinin HA1 chain | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | synthetic construct (others)![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, Y.J. / Veesler, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Antigen spacing on protein nanoparticles influences antibody responses to vaccination. Authors: Daniel Ellis / Annie Dosey / Seyhan Boyoglu-Barnum / Young-Jun Park / Rebecca Gillespie / Hubza Syeda / Geoffrey B Hutchinson / Yaroslav Tsybovsky / Michael Murphy / Deleah Pettie / Nick ...Authors: Daniel Ellis / Annie Dosey / Seyhan Boyoglu-Barnum / Young-Jun Park / Rebecca Gillespie / Hubza Syeda / Geoffrey B Hutchinson / Yaroslav Tsybovsky / Michael Murphy / Deleah Pettie / Nick Matheson / Sidney Chan / George Ueda / Jorge A Fallas / Lauren Carter / Barney S Graham / David Veesler / Masaru Kanekiyo / Neil P King / ![]() Abstract: Immunogen design approaches aim to control the specificity and quality of antibody responses elicited by next-generation vaccines. Here, we use computational protein design to generate a nanoparticle ...Immunogen design approaches aim to control the specificity and quality of antibody responses elicited by next-generation vaccines. Here, we use computational protein design to generate a nanoparticle vaccine platform based on the receptor-binding domain (RBD) of influenza hemagglutinin (HA) that enables precise control of antigen conformation and spacing. HA RBDs are presented as either monomers or native-like closed trimers that are connected to the underlying nanoparticle by a rigid linker that is modularly extended to precisely control antigen spacing. Nanoparticle immunogens with decreased spacing between trimeric RBDs elicit antibodies with improved hemagglutination inhibition and neutralization potency as well as binding breadth across diverse H1 HAs. Our "trihead" nanoparticle immunogen platform provides insights into anti-HA immunity, establishes antigen spacing as an important parameter in structure-based vaccine design, and embodies several design features that could be used in next-generation vaccines against influenza and other viruses. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.7 KB | Display | ![]() |
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PDB format | ![]() | 119.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 42486MC ![]() 8ur5C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 48580.578 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: I53_dn5 nanoparticle,I53_dn5 nanoparticle Source: (gene. exp.) synthetic construct (others), (gene. exp.) ![]() ![]() ![]() Gene: HA / Production host: ![]() ![]() #2: Sugar | ChemComp-NAG / ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
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Buffer solution | pH: 8 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||||||
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||
3D reconstruction![]() | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 399299 / Symmetry type: POINT |