8UR5

I53_dn5 nanoparticle displaying the trimeric HA heads with heptad domain, TH-1heptad-I53_dn5 (local refinement of TH-1heptad)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Antigen spacing on protein nanoparticles influences antibody responses to vaccination.

Ellis, D.Dosey, A.Boyoglu-Barnum, S.Park, Y.J.Gillespie, R.Syeda, H.Hutchinson, G.B.Tsybovsky, Y.Murphy, M.Pettie, D.Matheson, N.Chan, S.Ueda, G.Fallas, J.A.Carter, L.Graham, B.S.Veesler, D.Kanekiyo, M.King, N.P.

(2023) Cell Rep 42: 113552-113552

  • DOI: https://doi.org/10.1016/j.celrep.2023.113552
  • Primary Citation of Related Structures:  
    8UR5, 8UR7

  • PubMed 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 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.


  • Organizational Affiliation

    Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Trimer head HA,Hemagglutinin HA1 chain
A, B, C
388synthetic constructInfluenza A virusMutation(s): 10 
UniProt
Find proteins for Q289M7 (Influenza A virus (strain A/New Zealand:South Canterbury/35/2000 H1N1))
Explore Q289M7 
Go to UniProtKB:  Q289M7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ289M7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth C],
M [auth C],
N [auth C],
O [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01 AI167966

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release