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- EMDB-6796: CryoEM structure of HPV18 L1-only VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-6796
TitleCryoEM structure of HPV18 L1-only VLP
Map data
Sample
  • Virus: Alphapapillomavirus 7
Biological speciesAlphapapillomavirus 7
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsLi ZH / Yan XD / Zheng QB / Gu Y / Li SW
CitationJournal: Vaccine / Year: 2017
Title: Characterization of an Escherichia coli-derived human papillomavirus type 16 and 18 bivalent vaccine.
Authors: Ying Gu / Minxi Wei / Daning Wang / Zhihai Li / Minghui Xie / Huirong Pan / Ting Wu / Jun Zhang / Shaowei Li / Ningshao Xia /
Abstract: Human papillomavirus (HPV) types 16 and 18 account for approximately 70% of cervical cancer worldwide. Neutralizing HPV prophylactic vaccines offer significant benefit, as they block HPV infection ...Human papillomavirus (HPV) types 16 and 18 account for approximately 70% of cervical cancer worldwide. Neutralizing HPV prophylactic vaccines offer significant benefit, as they block HPV infection and prevent subsequent disease. However, the three licensed HPV vaccines that cover these two genotypes were produced in eukaryotic cells, which is expensive, particularly for low-income countries where HPV is highest. Here, we report a new HPV16 and -18 bivalent candidate vaccine produced from Escherichia coli. We used two strategies of N-terminal truncation of HPV L1 proteins and soluble non-fusion expression to generate HPV16 and HPV18 L1-only virus-like particles (VLPs) in a scalable process. Through comprehensive characterization of the bivalent candidate vaccine, we confirm lot consistency in a pilot scale-up of 30L, 100L and 500L. Using cryo-EM 3D reconstruction, we found that HPV16 and -18VLPs present in a T=7 icosahedral arrangement, similar in shape and size to that of the native virions. This HPV16/18 bivalent vaccine shares comparable immunogenicity with the licensed vaccines. Overall, we show that the production of a HPV16/18 bivalent vaccine from an E. coli expression system is robust and scalable, with potentially good accessibility worldwide as a population-based immunization strategy.
History
DepositionJul 15, 2017-
Header (metadata) releaseSep 6, 2017-
Map releaseSep 6, 2017-
UpdateSep 6, 2017-
Current statusSep 6, 2017Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_6796.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 4.44 Å
Density
Contour LevelBy AUTHOR: 1. / Movie #1: 1
Minimum - Maximum-4.1965246 - 7.800851
Average (Standard dev.)-0.000000000535577 (±1.)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-92-92-92
Dimensions180180180
Spacing180180180
CellA=B=C: 799.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.444.444.44
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z799.200799.200799.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-92-92-92
NC/NR/NS180180180
D min/max/mean-4.1977.801-0.000

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Supplemental data

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Sample components

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Entire : Alphapapillomavirus 7

EntireName: Alphapapillomavirus 7
Components
  • Virus: Alphapapillomavirus 7

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Supramolecule #1: Alphapapillomavirus 7

SupramoleculeName: Alphapapillomavirus 7 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 337042 / Sci species name: Alphapapillomavirus 7 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host systemOrganism: Escherichia coli (E. coli)

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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: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 1.4)
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 700

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