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- EMDB-31545: Engineered Hepatitis B virus core antigen with short linker T=4 -

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Basic information

Entry
Database: EMDB / ID: EMD-31545
TitleEngineered Hepatitis B virus core antigen with short linker T=4
Map data
SampleStaphylococcus aureus != Hepatitis B virus adr/Japan/Nishioka/1983

Staphylococcus aureus

  • Virus: Hepatitis B virus adr/Japan/Nishioka/1983
    • Protein or peptide: Capsid protein,Immunoglobulin G-binding protein A
Keywordscancer therapy / epidermal growth factor receptor 1 / affibody / VIRUS LIKE PARTICLE
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 / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding / extracellular region
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / LysM domain superfamily / Lysin motif / LysM domain ...Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / LysM domain superfamily / Lysin motif / 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 (strain Japan/adr4/1983) / Hepatitis B virus adr/Japan/Nishioka/1983
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsJeong H / Heo Y
Funding support Korea, Republic Of, 1 items
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, 2021-
Header (metadata) releaseSep 1, 2021-
Map releaseSep 1, 2021-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7fdj
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7fdj
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31545.png

Downloads & links

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Map

FileDownload / File: emd_31545.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 600 pix.
= 840. Å		1.4 Å/pix.
x 600 pix.
= 840. Å		1.4 Å/pix.
x 600 pix.
= 840. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-0.6116473 - 1.9016815
Average (Standard dev.)-0.0017753734 (±0.08717598)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 840.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z840.000840.000840.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.6121.902-0.002

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Supplemental data

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Sample components

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Entire : Staphylococcus aureus

EntireName: Staphylococcus aureus (bacteria)
Components
  • Virus: Hepatitis B virus adr/Japan/Nishioka/1983
    • Protein or peptide: Capsid protein,Immunoglobulin G-binding protein A

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Supramolecule #1: Hepatitis B virus adr/Japan/Nishioka/1983

SupramoleculeName: Hepatitis B virus adr/Japan/Nishioka/1983 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: virus core antigen with short linker / NCBI-ID: 482133 / Sci species name: Hepatitis B virus adr/Japan/Nishioka/1983 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Capsid protein,Immunoglobulin G-binding protein A

MacromoleculeName: Capsid protein,Immunoglobulin G-binding protein A / type: protein_or_peptide / ID: 1
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)
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis B virus genotype C subtype adr (strain Japan/adr4/1983)
Molecular weightTheoretical: 35.615 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHMAS SLRQILDSQK MEWRSNAGGS GGGSGGGTGG GGGGYYYYYY DIDPYKEFGA SVELLSFLPS DFFPSIRDLL DTASALYRE ALESPEHCSP HHTALRQAIL CWGELMNLAT WVGSNLEDLE VDNKFNKEMW AAWEEIRNLP NLNGWQMTAF I ASLVDDPS ...String:
MHHHHHHMAS SLRQILDSQK MEWRSNAGGS GGGSGGGTGG GGGGYYYYYY DIDPYKEFGA SVELLSFLPS DFFPSIRDLL DTASALYRE ALESPEHCSP HHTALRQAIL CWGELMNLAT WVGSNLEDLE VDNKFNKEMW AAWEEIRNLP NLNGWQMTAF I ASLVDDPS QSANLLAEAK KLNDAQAPKE FVDNKFNKEM WAAWEEIRNL PNLNGWQMTA FIASLVDDPS QSANLLAEAK KL NDAQAPK GSSRELVVSY VNVNMGLKIR QLLWFHISCL TFGRETVLEY LVSFGVWIRT PPAYRPPNAP ILSTLPETTV V

UniProtKB: Capsid protein, Immunoglobulin G-binding protein A, 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6bvf

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46346
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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