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- PDB-25ho: Cryo-EM structure of the Helicobacter pylori ferritin-I69C -

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Basic information

Entry
Database: PDB / ID: 25ho
TitleCryo-EM structure of the Helicobacter pylori ferritin-I69C
ComponentsBacterial non-heme ferritin
KeywordsSTRUCTURAL PROTEIN / Protein polymer / I69C / ferritin / nanoparticle
Function / homology
Function and homology information


bacterial non-heme ferritin / ferroxidase activity / ferric iron binding / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / identical protein binding / cytosol
Similarity search - Function
Ferritin, prokaryotic-type / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Bacterial non-heme ferritin
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsWang, N. / Liu, Y. / Shan, J. / Rao, H. / Ma, X. / Li, Y.
Funding support China, 3items
OrganizationGrant numberCountry
Other governmentGZNL2024A01017 China
Other governmentGZNL2025C01031 China
National Natural Science Foundation of China (NSFC)32500786 China
CitationJournal: J Nanobiotechnology / Year: 2026
Title: Rational design of an optimized ferritin nanoparticle vaccine targeting both SARS-CoV-2 and MERS-CoV.
Authors: Yaoming Liu / Haiyue Rao / Nana Wang / Xiaoqing Liu / Tao Chen / Bin Zhang / Jintao Lai / Jianyu Shan / Shiqi Xiao / Haojie Peng / Yiqiang Zhu / Taizhen Liang / Sen Liu / Meilin Hu / Lixiang ...Authors: Yaoming Liu / Haiyue Rao / Nana Wang / Xiaoqing Liu / Tao Chen / Bin Zhang / Jintao Lai / Jianyu Shan / Shiqi Xiao / Haojie Peng / Yiqiang Zhu / Taizhen Liang / Sen Liu / Meilin Hu / Lixiang Xie / Guochang Qiu / Xiaobo Li / Yaxin Li / Xiancai Ma /
Abstract: BACKGROUND: 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. ...BACKGROUND: 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.
RESULTS: 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 ...RESULTS: 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.
CONCLUSIONS: Our study demonstrated that rationally engineered HPF (I69C) produced highly stable and efficiently functionalized nanoparticle vaccines capable of eliciting potent humoral and cellular ...CONCLUSIONS: 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.
History
DepositionApr 3, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacterial non-heme ferritin
B: Bacterial non-heme ferritin
C: Bacterial non-heme ferritin
D: Bacterial non-heme ferritin
E: Bacterial non-heme ferritin
F: Bacterial non-heme ferritin
G: Bacterial non-heme ferritin
H: Bacterial non-heme ferritin
I: Bacterial non-heme ferritin
J: Bacterial non-heme ferritin
K: Bacterial non-heme ferritin
L: Bacterial non-heme ferritin
M: Bacterial non-heme ferritin
N: Bacterial non-heme ferritin
O: Bacterial non-heme ferritin
P: Bacterial non-heme ferritin
Q: Bacterial non-heme ferritin
R: Bacterial non-heme ferritin
S: Bacterial non-heme ferritin
T: Bacterial non-heme ferritin
U: Bacterial non-heme ferritin
V: Bacterial non-heme ferritin
W: Bacterial non-heme ferritin
X: Bacterial non-heme ferritin


Theoretical massNumber of molelcules
Total (without water)483,39824
Polymers483,39824
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Bacterial non-heme ferritin


Mass: 20141.568 Da / Num. of mol.: 24 / Mutation: I69C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: ftnA, pfr, jhp_0598 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZLI1, bacterial non-heme ferritin
Has protein modificationY

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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

ComponentName: Helicobacter pylori ferritin I69C / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Helicobacter pylori (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13PHENIX3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1501674 / Symmetry type: POINT
RefinementHighest resolution: 2.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00332496
ELECTRON MICROSCOPYf_angle_d0.45943848
ELECTRON MICROSCOPYf_dihedral_angle_d3.7514056
ELECTRON MICROSCOPYf_chiral_restr0.0364704
ELECTRON MICROSCOPYf_plane_restr0.0035664

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