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- PDB-8wjf: Peptide 10/FTH1 complex -

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Basic information

Entry
Database: PDB / ID: 8wjf
TitlePeptide 10/FTH1 complex
ComponentsPeptide 10,Ferritin heavy chain
KeywordsMETAL BINDING PROTEIN / Nano-delivery platform / De novo Design / Ferritin / Rabies virus Glycoprotein domain III (RABV-GDIII) / GDIII-Ferritin Nano-vaccine / stabilized / Strong immune response
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.02 Å
AuthorsFu, D. / Wang, M. / Guo, Y.
Funding support China, 1items
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, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_related / pdbx_entry_details / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update / _em_admin.title / _pdbx_database_related.details / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide 10,Ferritin heavy chain
B: Peptide 10,Ferritin heavy chain
C: Peptide 10,Ferritin heavy chain
D: Peptide 10,Ferritin heavy chain
E: Peptide 10,Ferritin heavy chain
F: Peptide 10,Ferritin heavy chain
G: Peptide 10,Ferritin heavy chain
H: Peptide 10,Ferritin heavy chain
I: Peptide 10,Ferritin heavy chain
J: Peptide 10,Ferritin heavy chain
K: Peptide 10,Ferritin heavy chain
L: Peptide 10,Ferritin heavy chain
M: Peptide 10,Ferritin heavy chain
N: Peptide 10,Ferritin heavy chain
O: Peptide 10,Ferritin heavy chain
P: Peptide 10,Ferritin heavy chain
Q: Peptide 10,Ferritin heavy chain
R: Peptide 10,Ferritin heavy chain
S: Peptide 10,Ferritin heavy chain
T: Peptide 10,Ferritin heavy chain
U: Peptide 10,Ferritin heavy chain
V: Peptide 10,Ferritin heavy chain
W: Peptide 10,Ferritin heavy chain
X: Peptide 10,Ferritin heavy chain


Theoretical massNumber of molelcules
Total (without water)566,16424
Polymers566,16424
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Peptide 10,Ferritin heavy chain


Mass: 23590.146 Da / Num. of mol.: 24 / Mutation: K87Q
Source method: isolated from a genetically manipulated source
Details: 1-16 : peptide 17-23 : linker / Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Colibacter (bacteria) / References: UniProt: P02794
Has protein modificationN

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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: Macromolecule: FTH1 Ligand: Peptide / Type: COMPLEX
Details: The structure of a complex comprising a 24-mer ferritin nanocage and 24 Peptides
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.9 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Colibacter (bacteria)
Buffer solutionpH: 8 / Details: 250mM NaCl, 50mM Tris-HCL, pH 8.0
Buffer component
IDConc.NameFormulaBuffer-ID
1250 mmol/Lsodium chlorideNaCl1
250 mmol/LTrishydroxymethylaminomeTris1
SpecimenConc.: 1.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 0.001 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 1 sec. / Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 1393

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.0.1particle selection
2EPUimage acquisition
4cryoSPARCv4.0.1CTF correction
7UCSF ChimeraX1.6.1.0model fitting
9cryoSPARCv4.0.1initial Euler assignment
10cryoSPARCv4.0.1final Euler assignment
11cryoSPARCv4.0.1classification
12cryoSPARCv4.0.13D reconstruction
13PHENIX1.15.2_3472:model refinement
CTF correctionDetails: CTF amplitude correction was performed following 3D reconstruction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 593434
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 2.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 516754 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 88.3 / Protocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00637849
ELECTRON MICROSCOPYf_angle_d0.59150977
ELECTRON MICROSCOPYf_dihedral_angle_d2.51422897
ELECTRON MICROSCOPYf_chiral_restr0.0395376
ELECTRON MICROSCOPYf_plane_restr0.0036744

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