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- EMDB-37578: Peptide 10/FTH1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-37578
TitlePeptide 10/FTH1 complex
Map data
Sample
  • Complex: Macromolecule: FTH1 Ligand: Peptide
    • Protein or peptide: Peptide 10,Ferritin heavy chain
KeywordsNano-delivery platform / De novo Design / Ferritin / Rabies virus Glycoprotein domain III (RABV-GDIII) / GDIII-Ferritin Nano-vaccine / stabilized / Strong immune response / METAL BINDING PROTEIN
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / ficolin-1-rich granule lumen / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / 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
Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.02 Å
AuthorsFu D / Wang M / Guo Y
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFE0200400 China
CitationJournal: Nat Commun / Year: 2024
Title: Self-assembling nanoparticle engineered from the ferritinophagy complex as a rabies virus vaccine candidate.
Authors: Dan Fu / Wenming Wang / Yan Zhang / Fan Zhang / Pinyi Yang / Chun Yang / Yufei Tian / Renqi Yao / Jingwu Jian / Zixian Sun / Nan Zhang / Zhiyu Ni / Zihe Rao / Lei Zhao / Yu Guo /
Abstract: Over the past decade, there has been a growing interest in ferritin-based vaccines due to their enhanced antigen immunogenicity and favorable safety profiles, with several vaccine candidates ...Over the past decade, there has been a growing interest in ferritin-based vaccines due to their enhanced antigen immunogenicity and favorable safety profiles, with several vaccine candidates targeting various pathogens advancing to phase I clinical trials. Nevertheless, challenges associated with particle heterogeneity, improper assembly and unanticipated immunogenicity due to the bulky protein adaptor have impeded further advancement. To overcome these challenges, we devise a universal ferritin-adaptor delivery platform based on structural insights derived from the natural ferritinophagy complex of the human ferritin heavy chain (FTH1) and the nuclear receptor coactivator 4 (NCOA4). The engineered ferritinophagy (Fagy)-tag peptide demonstrate significantly enhanced binding affinity to the 24-mer ferritin nanoparticle, enabling efficient antigen presentation. Subsequently, we construct a self-assembling rabies virus (RABV) vaccine candidate by noncovalently conjugating the Fagy-tagged glycoprotein domain III (G) of RABV to the ferritin nanoparticle, maintaining superior homogeneity, stability and immunogenicity. This vaccine candidate induces potent, rapid, and durable immune responses, and protects female mice against the authentic RABV challenge after single-dose administration. Furthermore, this universal, ferritin-based antigen conjugating strategy offers significant potential for developing vaccine against diverse pathogens and diseases.
History
DepositionSep 25, 2023-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37578.png

Downloads & links

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Map

FileDownload / File: emd_37578.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 320 pix.
= 220.8 Å		0.69 Å/pix.
x 320 pix.
= 220.8 Å		0.69 Å/pix.
x 320 pix.
= 220.8 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.076
Minimum - Maximum-0.15910754 - 0.53446376
Average (Standard dev.)-0.0019259911 (±0.047665413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 220.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37578_msk_1.map
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Half map: #2

Fileemd_37578_half_map_1.map
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Half map: #1

Fileemd_37578_half_map_2.map
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Sample components

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Entire : Macromolecule: FTH1 Ligand: Peptide

EntireName: Macromolecule: FTH1 Ligand: Peptide
Components
  • Complex: Macromolecule: FTH1 Ligand: Peptide
    • Protein or peptide: Peptide 10,Ferritin heavy chain

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Supramolecule #1: Macromolecule: FTH1 Ligand: Peptide

SupramoleculeName: Macromolecule: FTH1 Ligand: Peptide / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The structure of a complex comprising a 24-mer ferritin nanocage and 24 Peptides
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.9 kDa/nm

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Macromolecule #1: Peptide 10,Ferritin heavy chain

MacromoleculeName: Peptide 10,Ferritin heavy chain / type: protein_or_peptide / ID: 1 / Details: 1-16 : peptide 17-23 : linker / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.590146 KDa
Recombinant expressionOrganism: Colibacter (bacteria)
SequenceString: NTFEKIRNQP LSNFLAGGGS GGSMTTASTS QVRQNYHQDS EAAINRQINL ELYASYVYLS MSYYFDRDDV ALKNFAKYFL HQSHEEREH AEKLMKLQNQ RGGRIFLQDI QKPDCDDWES GLNAMECALH LEKNVNQSLL ELHKLATDKN DPHLCDFIET H YLNEQVKA ...String:
NTFEKIRNQP LSNFLAGGGS GGSMTTASTS QVRQNYHQDS EAAINRQINL ELYASYVYLS MSYYFDRDDV ALKNFAKYFL HQSHEEREH AEKLMKLQNQ RGGRIFLQDI QKPDCDDWES GLNAMECALH LEKNVNQSLL ELHKLATDKN DPHLCDFIET H YLNEQVKA IKELGDHVTN LRKMGAPESG LAEYLFDKHT LGDSDNES

UniProtKB: Ferritin heavy chain

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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

Concentration1.6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
250.0 mmol/LNaClsodium chloride
50.0 mmol/LTrisTrishydroxymethylaminome

Details: 250mM NaCl, 50mM Tris-HCL, pH 8.0
GridMaterial: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Pressure: 101.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 1393 / Average exposure time: 1.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 593434
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: O (octahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.0.1) / Number images used: 516754
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v4.0.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v4.0.1)
Final 3D classificationNumber classes: 1 / Avg.num./class: 516754 / Software - Name: cryoSPARC (ver. v4.0.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL / Overall B value: 88.3
Output model

PDB-8wjf:
Peptide 10/FTH1 complex

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