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- EMDB-6910: CryoEM structure of HPV58 L1-only VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-6910
TitleCryoEM structure of HPV58 L1-only VLP
Map data
Sample
  • Virus: Human papillomavirus type 58
Biological speciesHuman papillomavirus type 58
Methodsingle particle reconstruction / cryo EM / Resolution: 12.5 Å
AuthorsLi SW / Li ZH / He MZ
CitationJournal: Emerg Microbes Infect / Year: 2018
Title: N-terminal truncations on L1 proteins of human papillomaviruses promote their soluble expression in Escherichia coli and self-assembly in vitro.
Authors: Minxi Wei / Daning Wang / Zhihai Li / Shuo Song / Xianglin Kong / Xiaobing Mo / Yurou Yang / Maozhou He / Zhongyi Li / Bo Huang / Zhijie Lin / Huirong Pan / Qingbing Zheng / Hai Yu / Ying Gu ...Authors: Minxi Wei / Daning Wang / Zhihai Li / Shuo Song / Xianglin Kong / Xiaobing Mo / Yurou Yang / Maozhou He / Zhongyi Li / Bo Huang / Zhijie Lin / Huirong Pan / Qingbing Zheng / Hai Yu / Ying Gu / Jun Zhang / Shaowei Li / Ningshao Xia /
Abstract: Human papillomavirus (HPV) is the causative agent in genital warts and nearly all cervical, anogenital, and oropharyngeal cancers. Nine HPV types (6, 11, 16, 18, 31, 33, 45, 52, and 58) are ...Human papillomavirus (HPV) is the causative agent in genital warts and nearly all cervical, anogenital, and oropharyngeal cancers. Nine HPV types (6, 11, 16, 18, 31, 33, 45, 52, and 58) are associated with about 90% of cervical cancers and 90% of genital warts. HPV neutralization by vaccine-elicited neutralizing antibodies can block viral infection and prevent HPV-associated diseases. However, there is only one commercially available HPV vaccine, Gardasil 9, produced from Saccharomyces cerevisiae that covers all nine types, raising the need for microbial production of broad-spectrum HPV vaccines. Here, we investigated whether N-terminal truncations of the major HPV capsid proteins L1, improve their soluble expression in Escherichia coli. We found that N-terminal truncations promoted the soluble expression of HPV 33 (truncated by 10 amino acids [aa]), 52 (15 aa), and 58 (10 aa). The resultant HPV L1 proteins were purified in pentamer form and extensively characterized with biochemical, biophysical, and immunochemical methods. The pentamers self-assembled into virus-like particles (VLPs) in vitro, and 3D cryo-EM reconstructions revealed that all formed T = 7 icosahedral particles having 50-60-nm diameters. Moreover, we formulated a nine-valent HPV vaccine candidate with aluminum adjuvant and L1 VLPs from four genotypes used in this study and five from previous work. Immunogenicity assays in mice and non-human primates indicated that this HPV nine-valent vaccine candidate elicits neutralizing antibody titers comparable to those induced by Gardasil 9. Our study provides a method for producing a nine-valent HPV vaccine in E. coli and may inform strategies for the soluble expression of other vaccine candidates.
History
DepositionFeb 10, 2018-
Header (metadata) releaseOct 10, 2018-
Map releaseOct 10, 2018-
UpdateOct 10, 2018-
Current statusOct 10, 2018Processing 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
  • Download
  • 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_6910.png

Downloads & links

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Map

FileDownload / File: emd_6910.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-19.736858000000002 - 26.759968000000001
Average (Standard dev.)-0.000056223584 (±3.344422)
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-19.73726.760-0.000

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Supplemental data

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Sample components

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Entire : Human papillomavirus type 58

EntireName: Human papillomavirus type 58
Components
  • Virus: Human papillomavirus type 58

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Supramolecule #1: Human papillomavirus type 58

SupramoleculeName: Human papillomavirus type 58 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10598 / Sci species name: Human papillomavirus type 58 / 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: 12.5 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 536
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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