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

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Basic information

Entry
Database: PDB / ID: 8wjf
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
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 / intracellular sequestering of iron ion / ferroxidase activity / 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 / intracellular sequestering of iron ion / ferroxidase activity / 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: 2.02 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: 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

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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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