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- EMDB-34155: Designed pH-responsive P22 VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-34155
TitleDesigned pH-responsive P22 VLP
Map data
Sample
  • Virus: Lederbergvirus
    • Protein or peptide: Major capsid protein
KeywordsP22 coat protein / designed protein / VIRUS LIKE PARTICLE
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
Methodsingle particle reconstruction / cryo EM / Resolution: 4.02 Å
AuthorsKim KJ / Kim G / Bae JH / Song JJ / Kim HS
Funding support Korea, Republic Of, 1 items
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, 2022-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34155.png

Downloads & links

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Map

FileDownload / File: emd_34155.map.gz / Format: CCP4 / Size: 12.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.2995 Å
Density
Contour LevelBy AUTHOR: 0.0949
Minimum - Maximum-0.7025786 - 0.97285473
Average (Standard dev.)-0.000000000000542 (±0.07290584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions154163134
Spacing134154163
CellA: 174.133 Å / B: 200.123 Å / C: 211.8185 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34155_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34155_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Lederbergvirus

EntireName: Lederbergvirus
Components
  • Virus: Lederbergvirus
    • Protein or peptide: Major capsid protein

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Supramolecule #1: Lederbergvirus

SupramoleculeName: Lederbergvirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 186794 / Sci species name: Lederbergvirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes
Host (natural)Organism: Lederbergvirus

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Lederbergvirus
Molecular weightTheoretical: 46.40118 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: NEGQIVTLAV DEIIETISAI TPMAQKAKKY TPPAASMQRH SNTIWMPVEQ HSPTQEGWDL TDKATGLLEL NVAVNMGEPD NDFFQLRAD DLRDETAYRR RIQSAARKLA NNVELKVANM AAEMGSLVIT SPDAIGTNTA DAWNFVADAE HIMFSRELNR D MGTSYFFN ...String:
NEGQIVTLAV DEIIETISAI TPMAQKAKKY TPPAASMQRH SNTIWMPVEQ HSPTQEGWDL TDKATGLLEL NVAVNMGEPD NDFFQLRAD DLRDETAYRR RIQSAARKLA NNVELKVANM AAEMGSLVIT SPDAIGTNTA DAWNFVADAE HIMFSRELNR D MGTSYFFN PQDYKKAGYD LTKRDIFGRI PEEAYRDGTI QRQVAGFDDV LRSPKLPVLT KSTATGITVS GAQSFKPVAW QL DNDGNKV NVDNRFATVT LSATTGMKRG DKISFAGVKF LGQMAKHVLA QDATFSVVRV VDGTHVEITP KPVALDDVSL SPE QRAYAN VNTSLADAMA VNILNVKDAR TNVFWADDAI RIVSQPIPAN HELFAGMKTT SFSIPDVGLN GIFATQGDIS TLSG LCRIA LWYGVNATRP EAIGVGLPGQ

UniProtKB: Major capsid protein

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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

Concentration17 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClsodium chloride
2.7 mMKClpotassium chloride
8.0 mMNa2HPO4Sodium hydrogen phosphate
2.0 mMKH2PO4Potassium dihydrogen phosphate

Details: PBS buffer pH 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: The grid was glow discharged at 15 mA for 1 min.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1654 / Average exposure time: 52.69 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 92000

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Image processing

Particle selectionNumber selected: 25282
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX
Software - details: density modification was carried out at PHENIX
Number images used: 3320
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

5uu5


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

PDB-8gn5:
Designed pH-responsive P22 VLP

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