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- PDB-8wiq: Unlocking Immunogenic Potential: Innovating a Peptide/Ferritin Fu... -

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Basic information

Entry
Database: PDB / ID: 8wiq
TitleUnlocking Immunogenic Potential: Innovating a Peptide/Ferritin Fusion Tag Nano-Delivery Platform from de novo design to Significantly Enhance Antigenicity of the Rabies Virus Glycoprotein Domain III
ComponentsNative peptide,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 / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation ...iron ion sequestering activity / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation / autophagosome / ferric iron binding / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / 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: 2.19 Å
AuthorsFu, D. / Wang, M. / Guo, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFE0200400 China
CitationJournal: To Be Published
Title: Unlocking Immunogenic Potential: Innovating a Peptide/Ferritin Fusion Tag Nano-Delivery Platform from de novo design to Significantly Enhance Antigenicity of the Rabies Virus Glycoprotein Domain III
Authors: Fu, D. / Wang, M. / Guo, Y.
History
DepositionSep 25, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)565,75524
Polymers565,75524
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 ...
Native peptide,Ferritin heavy chain


Mass: 23573.133 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

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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 overall structure of the complex can be described as consisting of self-assembled human ferritin 24-mer and 24 peptides.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 2.3 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 mM/Lsodium chlorideNaCl1
250 mM/LTrishydroxymethylaminomethaneTris1
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: DARK 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: 1220

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4particle selection
2PHENIX1.15.2_3472:model refinement
3EPUimage acquisition
5cryoSPARCv4CTF correction
12cryoSPARCv4classification
13cryoSPARCv43D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 457025
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 434794 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00437848
ELECTRON MICROSCOPYf_angle_d0.71151024
ELECTRON MICROSCOPYf_dihedral_angle_d11.81222824
ELECTRON MICROSCOPYf_chiral_restr0.0425400
ELECTRON MICROSCOPYf_plane_restr0.0046696

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