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- EMDB-6797: CryoEM structure of HPV6 L1-only VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-6797
TitleCryoEM structure of HPV6 L1-only VLP
Map data
Sample
  • Virus: Alphapapillomavirus 10
Biological speciesAlphapapillomavirus 10
Methodsingle particle reconstruction / cryo EM / Resolution: 30.0 Å
AuthorsLi SW
CitationJournal: Vaccine / Year: 2017
Title: Bacterially expressed human papillomavirus type 6 and 11 bivalent vaccine: Characterization, antigenicity and immunogenicity.
Authors: Huirong Pan / Zhihai Li / Jin Wang / Shuo Song / Daning Wang / Minxi Wei / Ying Gu / Jun Zhang / Shaowei Li / Ningshao Xia /
Abstract: Human papillomavirus (HPV)-6 and HPV11 are the major etiological causes of condylomata acuminate. HPV neutralization by vaccine-elicited neutralizing antibodies can block viral infection and prevent ...Human papillomavirus (HPV)-6 and HPV11 are the major etiological causes of condylomata acuminate. HPV neutralization by vaccine-elicited neutralizing antibodies can block viral infection and prevent subsequent disease. Currently, two commercially available HPV vaccines cover these two genotypes, expressed by Saccharomyces cerevisiae. Here we describe another HPV6/11 bivalent vaccine candidate derived from Escherichia coli. The soluble expression of N-terminally truncated L1 proteins was optimized to generate HPV6- and HPV11 L1-only virus-like particles (VLPs) as a scalable process. In a pilot scale, we used various biochemical, biophysical and immunochemical approaches to comprehensively characterize the scale and lot consistency of the vaccine candidate at 30L and 100L. Cryo-EM structure analysis showed that these VLPs form a T=7 icosahedral lattice, imitating the L1 capsid of the authentic HPV virion. This HPV6/11 bivalent vaccine confers a neutralization titer and antibody production profile in monkey that is comparable with the quadrivalent vaccine, Gardasil. This study demonstrates the robustness and scalability of a potential HPV6/11 bivalent vaccine using a prokaryotic system for vaccine production.
History
DepositionJul 15, 2017-
Header (metadata) releaseAug 23, 2017-
Map releaseAug 23, 2017-
UpdateAug 23, 2017-
Current statusAug 23, 2017Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6797.png

Downloads & links

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Map

FileDownload / File: emd_6797.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.44 Å/pix.
x 180 pix.
= 799.2 Å		4.44 Å/pix.
x 180 pix.
= 799.2 Å		4.44 Å/pix.
x 180 pix.
= 799.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2. / Movie #1: 2
Minimum - Maximum-3.5920298 - 4.9232173
Average (Standard dev.)0.000000002374154 (±1.)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-90-90-90
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-90-90-90
NC/NR/NS180180180
D min/max/mean-3.5924.9230.000

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Supplemental data

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Sample components

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Entire : Alphapapillomavirus 10

EntireName: Alphapapillomavirus 10
Components
  • Virus: Alphapapillomavirus 10

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Supramolecule #1: Alphapapillomavirus 10

SupramoleculeName: Alphapapillomavirus 10 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 333754 / Sci species name: Alphapapillomavirus 10 / 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: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 365
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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