25HO | pdb_000025ho

Cryo-EM structure of the Helicobacter pylori ferritin-I69C


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 25HO

This is version 1.0 of the entry. See complete history

Literature

Rational design of an optimized ferritin nanoparticle vaccine targeting both SARS-CoV-2 and MERS-CoV.

Liu, Y.Rao, H.Wang, N.Liu, X.Chen, T.Zhang, B.Lai, J.Shan, J.Xiao, S.Peng, H.Zhu, Y.Liang, T.Liu, S.Hu, M.Xie, L.Qiu, G.Li, X.Li, Y.Ma, X.

(2026) J Nanobiotechnology 

  • DOI: https://doi.org/10.1186/s12951-026-04738-y
  • Primary Citation Related Structures: 
    25HO

  • PubMed Abstract: 

    Coronaviruses including SARS-CoV-2 and MERS-CoV remain threats to global health. Ferritin nanoparticle-based vaccines are promising platforms for coronaviral multivalent antigen display. However, their development is often constrained by limited stability and homogeneity, which hinders scale-up manufacturing and long-term storage. Here, we employed artificial intelligence (AI)-guided structural modeling and optimization to introduce disulfide bonds into Helicobacter pylori ferritin (HPF). Cryo-EM at 2.2 Å confirmed the formation of inter-subunit disulfide bonds in the most promising variant HPF (I69C), resulting in a more homogeneous nanoparticle with enhanced thermal and pH stability, as well as improved solubility in physiological conditions. We utilized the ST003/SC003 molecular glue system to covalently conjugate receptor-binding domains (RBDs) of both SARS-CoV-2 and MERS-CoV, either as a mixture of individual RBD-HPF (I69C) particles or as a dimeric RBD displayed on a single HPF (I69C). Both bivalent nanoparticle vaccines elicited significantly higher titers of RBD-specific antibodies and neutralizing antibodies compared to monomeric and dimeric vaccines. Vaccination also increased frequencies of antigen-specific B cells and polyfunctional CD4 + and CD8 + T cells. No vaccine-related systemic abnormalities were observed. In both hACE2 and hDPP4 transgenic mice, two doses of bivalent nanoparticle vaccines provided protection against authentic SARS-CoV-2 and MERS-CoV challenges. Our study demonstrated that rationally engineered HPF (I69C) produced highly stable and efficiently functionalized nanoparticle vaccines capable of eliciting potent humoral and cellular immune responses against both SARS-CoV-2 and MERS-CoV infection, thereby supporting the further development of bivalent nanoparticle vaccine platforms.


  • Organizational Affiliation
    • College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.

Macromolecule Content 

  • Total Structure Weight: 483.4 kDa 
  • Atom Count: 31,776 
  • Modeled Residue Count: 3,888 
  • Deposited Residue Count: 4,152 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bacterial non-heme ferritin
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
173Helicobacter pyloriMutation(s): 1 
Gene Names: ftnApfrjhp_0598
EC: 1.16.3.2
UniProt
Find proteins for Q9ZLI1 (Helicobacter pylori (strain J99 / ATCC 700824))
Explore Q9ZLI1 
Go to UniProtKB:  Q9ZLI1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZLI1
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChinaGZNL2024A01017
Other governmentChinaGZNL2025C01031
National Natural Science Foundation of China (NSFC)China32500786

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-08
    Type: Initial release