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- PDB-7fdj: Engineered Hepatitis B virus core antigen with short linker T=4 -

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Basic information

Entry
Database: PDB / ID: 7fdj
TitleEngineered Hepatitis B virus core antigen with short linker T=4
ComponentsCapsid protein,Immunoglobulin G-binding protein A
KeywordsVIRUS LIKE PARTICLE / cancer therapy / epidermal growth factor receptor 1 / affibody
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / IgG binding / viral penetration into host nucleus / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding / extracellular region
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain ...Octapeptide repeat / Octapeptide repeat / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Immunoglobulin G-binding protein A / Capsid protein
Similarity search - Component
Biological speciesHepatitis B virus genotype C subtype adr
Staphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsJeong, H. / Heo, Y. / Yoo, Y. / Ryu, B. / Yun, J. / Cho, H. / Lee, W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Int J Mol Sci / Year: 2021
Title: Structural and Functional Characterizations of Cancer Targeting Nanoparticles Based on Hepatitis B Virus Capsid.
Authors: Yunseok Heo / Hyeongseop Jeong / Youngki Yoo / Ji-Hye Yun / Bumhan Ryu / Young-Je Cha / Bo-Ram Lee / Ye-Eun Jeon / Jongmin Kim / Sojin Jeong / Eunji Jo / Jae-Sung Woo / Jeewon Lee / Hyun-Soo Cho / Weontae Lee /
Abstract: Cancer targeting nanoparticles have been extensively studied, but stable and applicable agents have yet to be developed. Here, we report stable nanoparticles based on hepatitis B core antigen (HBcAg) ...Cancer targeting nanoparticles have been extensively studied, but stable and applicable agents have yet to be developed. Here, we report stable nanoparticles based on hepatitis B core antigen (HBcAg) for cancer therapy. HBcAg monomers assemble into spherical capsids of 180 or 240 subunits. HBcAg was engineered to present an affibody for binding to human epidermal growth factor receptor 1 (EGFR) and to present histidine and tyrosine tags for binding to gold ions. The HBcAg engineered to present affibody and tags (HAF) bound specifically to EGFR and exterminated the EGFR-overexpressing adenocarcinomas under alternating magnetic field (AMF) after binding with gold ions. Using cryogenic electron microscopy (cryo-EM), we obtained the molecular structures of recombinant HAF and found that the overall structure of HAF was the same as that of HBcAg, except with the affibody on the spike. Therefore, HAF is viable for cancer therapy with the advantage of maintaining a stable capsid form. If the affibody in HAF is replaced with a specific sequence to bind to another targetable disease protein, the nanoparticles can be used for drug development over a wide spectrum.
History
DepositionJul 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-31545
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  • Superimposition on EM map
  • EMDB-31545
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein,Immunoglobulin G-binding protein A
B: Capsid protein,Immunoglobulin G-binding protein A
D: Capsid protein,Immunoglobulin G-binding protein A
C: Capsid protein,Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)142,4604
Polymers142,4604
Non-polymers00
Water0
1
A: Capsid protein,Immunoglobulin G-binding protein A
B: Capsid protein,Immunoglobulin G-binding protein A
D: Capsid protein,Immunoglobulin G-binding protein A
C: Capsid protein,Immunoglobulin G-binding protein A
x 60


Theoretical massNumber of molelcules
Total (without water)8,547,600240
Polymers8,547,600240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein,Immunoglobulin G-binding protein A
B: Capsid protein,Immunoglobulin G-binding protein A
D: Capsid protein,Immunoglobulin G-binding protein A
C: Capsid protein,Immunoglobulin G-binding protein A
x 5


  • icosahedral pentamer
  • 712 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)712,30020
Polymers712,30020
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein,Immunoglobulin G-binding protein A
B: Capsid protein,Immunoglobulin G-binding protein A
D: Capsid protein,Immunoglobulin G-binding protein A
C: Capsid protein,Immunoglobulin G-binding protein A
x 6


  • icosahedral 23 hexamer
  • 855 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)854,76024
Polymers854,76024
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Antibody
Capsid protein,Immunoglobulin G-binding protein A / / Core antigen / Core protein / HBcAg / p21.5 / IgG-binding protein A / Staphylococcal protein A / SpA


Mass: 35615.000 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: MHHHHHHMASSLRQILDSQKMEWRSNAGGSGGGSGGGTGGGGGGYYYYYY (expression tag) DIDPYKEFGASVELLSFLPSDFFPSIRDLLDTASALYREALESPEHCSPHHTALRQAILCWGELMNLATWVGSNLED (P69706, residues 2-78) LE (linker) ...Details: MHHHHHHMASSLRQILDSQKMEWRSNAGGSGGGSGGGTGGGGGGYYYYYY (expression tag) DIDPYKEFGASVELLSFLPSDFFPSIRDLLDTASALYREALESPEHCSPHHTALRQAILCWGELMNLATWVGSNLED (P69706, residues 2-78) LE (linker) VDNKFNKEMWAAWEEIRNLPNLNGWQMTAFIASLVDDPSQSANLLAEAKKLNDAQAPK (P38507, residues 212-269 => modified) EF (linker) VDNKFNKEMWAAWEEIRNLPNLNGWQMTAFIASLVDDPSQSANLLAEAKKLNDAQAPK (P38507, residues 212-269 => modified) GS (linker) SRELVVSYVNVNMGLKIRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILSTLPETTVV (P69706, residues 81-149)
Source: (gene. exp.) Hepatitis B virus genotype C subtype adr (strain Japan/adr4/1983), (gene. exp.) Staphylococcus aureus (bacteria)
Gene: spa / Production host: Escherichia coli (E. coli) / References: UniProt: P69706, UniProt: P38507

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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: Staphylococcus aureus / Type: VIRUS / Details: virus core antigen with short linker / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Hepatitis B virus adr/Japan/Nishioka/1983482133
21Staphylococcus aureus (bacteria)1280
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46346 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034552
ELECTRON MICROSCOPYf_angle_d0.6516224
ELECTRON MICROSCOPYf_dihedral_angle_d4.502596
ELECTRON MICROSCOPYf_chiral_restr0.041696
ELECTRON MICROSCOPYf_plane_restr0.004780

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