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- EMDB-0878: HPV chVLP -

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Basic information

Entry
Database: EMDB / ID: EMD-0878
TitleHPV chVLP
Map data
Sample
  • Virus: Human papillomavirus
Biological speciesHuman papillomavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 26.1 Å
AuthorsLi SW / Liu XL
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaU1705283 China
National Natural Science Foundation of China81701637 China
Other government2018ZX09738008 China
CitationJournal: Nat Commun / Year: 2020
Title: Rational design of a multi-valent human papillomavirus vaccine by capsomere-hybrid co-assembly of virus-like particles.
Authors: Daning Wang / Xinlin Liu / Minxi Wei / Ciying Qian / Shuo Song / Jie Chen / Zhiping Wang / Qin Xu / Yurou Yang / Maozhou He / Xin Chi / Shiwen Huang / Tingting Li / Zhibo Kong / Qingbing ...Authors: Daning Wang / Xinlin Liu / Minxi Wei / Ciying Qian / Shuo Song / Jie Chen / Zhiping Wang / Qin Xu / Yurou Yang / Maozhou He / Xin Chi / Shiwen Huang / Tingting Li / Zhibo Kong / Qingbing Zheng / Hai Yu / Yingbin Wang / Qinjian Zhao / Jun Zhang / Ningshao Xia / Ying Gu / Shaowei Li /
Abstract: The capsid of human papillomavirus (HPV) spontaneously arranges into a T = 7 icosahedral particle with 72 L1 pentameric capsomeres associating via disulfide bonds between Cys175 and Cys428. Here, ...The capsid of human papillomavirus (HPV) spontaneously arranges into a T = 7 icosahedral particle with 72 L1 pentameric capsomeres associating via disulfide bonds between Cys175 and Cys428. Here, we design a capsomere-hybrid virus-like particle (chVLP) to accommodate multiple types of L1 pentamers by the reciprocal assembly of single C175A and C428A L1 mutants, either of which alone encumbers L1 pentamer particle self-assembly. We show that co-assembly between any pair of C175A and C428A mutants across at least nine HPV genotypes occurs at a preferred equal molar stoichiometry, irrespective of the type or number of L1 sequences. A nine-valent chVLP vaccine-formed through the structural clustering of HPV epitopes-confers neutralization titers that are comparable with that of Gardasil 9 and elicits minor cross-neutralizing antibodies against some heterologous HPV types. These findings may pave the way for a new vaccine design that targets multiple pathogenic variants or cancer cells bearing diverse neoantigens.
History
DepositionDec 3, 2019-
Header (metadata) releaseMay 6, 2020-
Map releaseMay 6, 2020-
UpdateMay 26, 2021-
Current statusMay 26, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0878.png

Downloads & links

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Map

FileDownload / File: emd_0878.map.gz / Format: CCP4 / Size: 2.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.128 Å
Density
Contour LevelBy AUTHOR: 8.0 / Movie #1: 5
Minimum - Maximum-18.506945 - 20.636562
Average (Standard dev.)-0.08893871 (±2.244991)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-410-410-410
Dimensions821821821
Spacing821821821
CellA=B=C: 926.088 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1281.1281.128
M x/y/z821821821
origin x/y/z0.0000.0000.000
length x/y/z926.088926.088926.088
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-410-410-410
NC/NR/NS821821821
D min/max/mean-18.50720.637-0.089

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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 (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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (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

Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 26.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 278

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