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- PDB-8gn5: Designed pH-responsive P22 VLP -

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Basic information

Entry
Database: PDB / ID: 8gn5
TitleDesigned pH-responsive P22 VLP
ComponentsMajor capsid protein
KeywordsVIRUS LIKE PARTICLE / P22 coat protein / designed protein
Function / homologyMajor capsid protein Gp5 / P22 coat protein - gene protein 5 / viral procapsid / viral procapsid maturation / T=7 icosahedral viral capsid / viral capsid / identical protein binding / Major capsid protein
Function and homology information
Biological speciesLederbergvirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.02 Å
AuthorsKim, K.J. / Kim, G. / Bae, J.H. / Song, J.J. / Kim, H.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Adv Healthc Mater / Year: 2024
Title: A pH-Responsive Virus-Like Particle as a Protein Cage for a Targeted Delivery.
Authors: Kwan-Jip Kim / Gijeong Kim / Jin-Ho Bae / Ji-Joon Song / Hak-Sung Kim /
Abstract: A stimuli-responsive protein self-assembly offers promising utility as a protein nanocage for biotechnological and medical applications. Herein, the development of a virus-like particle (VLP) that ...A stimuli-responsive protein self-assembly offers promising utility as a protein nanocage for biotechnological and medical applications. Herein, the development of a virus-like particle (VLP) that undergoes a transition between assembly and disassembly under a neutral and acidic pH, respectively, for a targeted delivery is reported. The structure of the bacteriophage P22 coat protein is used for the computational design of coat subunits that self-assemble into a pH-responsive VLP. Subunit designs are generated through iterative computational cycles of histidine substitutions and evaluation of the interaction energies among the subunits under an acidic and neutral pH. The top subunit designs are tested and one that is assembled into a VLP showing the highest pH-dependent structural transition is selected. The cryo-EM structure of the VLP is determined, and the structural basis of a pH-triggered disassembly is delineated. The utility of the designed VLP is exemplified through the targeted delivery of a cytotoxic protein cargo into tumor cells in a pH-dependent manner. These results provide strategies for the development of self-assembling protein architectures with new functionality for diverse applications.
History
DepositionAug 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)185,6054
Polymers185,6054
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Major capsid protein / Gene product 5 / gp5 / Major head protein


Mass: 46401.180 Da / Num. of mol.: 4 / Mutation: S43H, E54H, E153H, N287H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lederbergvirus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P26747

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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: Lederbergvirus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Lederbergvirus
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Details of virusEmpty: YES / Enveloped: YES / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Lederbergvirus
Buffer solutionpH: 7.4 / Details: PBS buffer pH 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1137 mMsodium chlorideNaCl1
22.7 mMpotassium chlorideKCl1
38 mMSodium hydrogen phosphateNa2HPO41
42 mMPotassium dihydrogen phosphateKH2PO41
SpecimenConc.: 17 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: The grid was glow discharged at 15 mA for 1 min. / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 288 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 92000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingAverage exposure time: 52.69 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1654

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Processing

EM software
IDNameCategoryDetails
1crYOLOparticle selection
4RELIONCTF correction
7UCSF Chimeramodel fitting
9ISOLDEmodel refinement
10PHENIXmodel refinement
14PHENIX3D reconstructiondensity modification was carried out at PHENIX
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 25282
3D reconstructionResolution: 4.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3320 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 5UU5

5uu5


Accession code: 5UU5 / Source name: PDB / Type: experimental model

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