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- EMDB-9920: The cryo-em structure of HPV18 VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-9920
TitleThe cryo-em structure of HPV18 VLP
Map dataThe cryo-em structure of HPV18 VLP
Sample
  • Virus: Human papillomavirus
Biological speciesHuman papillomavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 11.5 Å
AuthorsLi S / Zheng Q
CitationJournal: Eur J Pharm Biopharm / Year: 2019
Title: Altered antigenicity and immunogenicity of human papillomavirus virus-like particles in the presence of thimerosal.
Authors: Siyi Chen / Xiaofen Huang / Yike Li / Xin Wang / Huirong Pan / Zhijie Lin / Qingbing Zheng / Shaowei Li / Jun Zhang / Ningshao Xia / Qinjian Zhao /
Abstract: Thimerosal has been widely used as a preservative in human vaccines for decades. Thimerosal, a thiol capping agent with ethyl mercury being the active degradant, could have impacts on the vaccine ...Thimerosal has been widely used as a preservative in human vaccines for decades. Thimerosal, a thiol capping agent with ethyl mercury being the active degradant, could have impacts on the vaccine potency due to potential thiol modification. The effects on the antigenicity and immunogenicity of human papillomavirus (HPV) virus-like particles (VLPs) in the presence of thimerosal was studied. In general, reduced binding activity was observed between HPV antigens and monoclonal antibodies (mAbs) upon thimerosal treatment, accompanied by reduced protein conformational stability. The immunogenicity of a pentavalent vaccine formulation (HPV6, HPV11, HPV16, HPV18 and hepatitis E virus) with or without thimerosal was studied in mice. The functional antibody titres, as well as the binding titres, were determined, showing a substantial decrease for vaccine formulations containing thimerosal for HPV16/18. Similarly, epitope-specific competition assays using specific and functional mAbs as tracers also showed a significant reduction in immunogenicity for HPV16/18 in the presence of thimerosal. Structural alterations in the capsid protein for HPV18 were observed with cryo-electron microscopy and 3-dimensional reconstruction in the comparative structural analysis. The results should alert scientists in formulation development field on the choice for vaccine preservatives, in particular for thiol-containing antigens.
History
DepositionJun 1, 2019-
Header (metadata) releaseJul 10, 2019-
Map releaseJul 10, 2019-
UpdateJan 22, 2020-
Current statusJan 22, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 50
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 50
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9920.png

Downloads & links

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Map

FileDownload / File: emd_9920.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe cryo-em structure of HPV18 VLP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 801 pix.
= 903.528 Å		1.13 Å/pix.
x 801 pix.
= 903.528 Å		1.13 Å/pix.
x 801 pix.
= 903.528 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.128 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 50 / Movie #1: 50
Minimum - Maximum-251.42459 - 324.41013
Average (Standard dev.)0.24942526 (±33.92373)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-400-400-400
Dimensions801801801
Spacing801801801
CellA=B=C: 903.528 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1281.1281.128
M x/y/z801801801
origin x/y/z0.0000.0000.000
length x/y/z903.528903.528903.528
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-400-400-400
NC/NR/NS801801801
D min/max/mean-251.425324.4100.249

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Supplemental data

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Sample components

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Entire : Human papillomavirus

EntireName: Human papillomavirus
Components
  • Virus: Human papillomavirus

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Supramolecule #1: Human papillomavirus

SupramoleculeName: Human papillomavirus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10566 / Sci species name: Human papillomavirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host systemOrganism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)

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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

Concentration2.0 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 11.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 901

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