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- EMDB-80106: Cryo-EM structure of the Helicobacter pylori ferritin-I69C -

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Basic information

Entry
Database: EMDB / ID: EMD-80106
TitleCryo-EM structure of the Helicobacter pylori ferritin-I69C
Map data
Sample
  • Complex: Helicobacter pylori ferritin I69C
    • Protein or peptide: Bacterial non-heme ferritin
KeywordsProtein polymer / I69C / ferritin / nanoparticle / structural protein
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsWang N / Liu Y / Shan J / Rao H / Ma X / Li Y
Funding support China, 3 items
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, 2026-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80106.png

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Map

FileReleased
Projections & slices

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Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 256 pix.
= 186.88 Å		0.73 Å/pix.
x 256 pix.
= 186.88 Å		0.73 Å/pix.
x 256 pix.
= 186.88 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.56
Minimum - Maximum-1.5681646 - 2.092593
Average (Standard dev.)0.0029680931 (±0.14623266)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 186.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_80106_msk_1.map
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Half map: #2

Fileemd_80106_half_map_1.map
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Half map: #1

Fileemd_80106_half_map_2.map
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Sample components

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Entire : Helicobacter pylori ferritin I69C

EntireName: Helicobacter pylori ferritin I69C
Components
  • Complex: Helicobacter pylori ferritin I69C
    • Protein or peptide: Bacterial non-heme ferritin

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Supramolecule #1: Helicobacter pylori ferritin I69C

SupramoleculeName: Helicobacter pylori ferritin I69C / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Helicobacter pylori (bacteria)

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Macromolecule #1: Bacterial non-heme ferritin

MacromoleculeName: Bacterial non-heme ferritin / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: bacterial non-heme ferritin
Source (natural)Organism: Helicobacter pylori (bacteria)
Molecular weightTheoretical: 20.141568 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGDIIKLLNE QVNKEMQSSN LYMSMSSWCY THSLDGAGLF LFDHAAEEYE HAKKLIIFLN ENNVPVQLTS CSAPEHKFEG LTQIFQKAY EHEQHISESI NNIVDHAIKS KDHATFNFLQ WYVAEQHEEE VLFKDILDKI ELIGNENHGL YLADQYVKGI A KSRKSLEH HHHHH

UniProtKB: Bacterial non-heme ferritin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 1501674
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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