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- EMDB-37578: Unlocking Immunogenic Potential: Innovating a Peptide/Ferritin Fu... -

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Basic information

Entry
Database: EMDB / ID: EMD-37578
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
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 / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / 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)
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: 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, 2023-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing 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

Slices (1/3)

Slices (1/2)

Slices (2/3)

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
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37578_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37578_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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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:
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

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