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- EMDB-9665: The cryoEM map of HPV33 VLP in complex with the Fab fragment of a... -

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Basic information

Entry
Database: EMDB / ID: EMD-9665
TitleThe cryoEM map of HPV33 VLP in complex with the Fab fragment of antibody 4E5
Map data
Sample
  • Virus: Human papillomavirus type 33
Biological speciesHuman papillomavirus type 33
Methodsingle particle reconstruction / cryo EM / Resolution: 12.3 Å
AuthorsLi ZH / Song S / He MZ / Gu Y / Li SW
CitationJournal: Nat Commun / Year: 2018
Title: Rational design of a triple-type human papillomavirus vaccine by compromising viral-type specificity.
Authors: Zhihai Li / Shuo Song / Maozhou He / Daning Wang / Jingjie Shi / Xinlin Liu / Yunbing Li / Xin Chi / Shuangping Wei / Yurou Yang / Zhiping Wang / Jinjin Li / Huilian Qian / Hai Yu / Qingbing ...Authors: Zhihai Li / Shuo Song / Maozhou He / Daning Wang / Jingjie Shi / Xinlin Liu / Yunbing Li / Xin Chi / Shuangping Wei / Yurou Yang / Zhiping Wang / Jinjin Li / Huilian Qian / Hai Yu / Qingbing Zheng / Xiaodong Yan / Qinjian Zhao / Jun Zhang / Ying Gu / Shaowei Li / Ningshao Xia /
Abstract: Sequence variability in surface-antigenic sites of pathogenic proteins is an important obstacle in vaccine development. Over 200 distinct genomic sequences have been identified for human ...Sequence variability in surface-antigenic sites of pathogenic proteins is an important obstacle in vaccine development. Over 200 distinct genomic sequences have been identified for human papillomavirus (HPV), of which more than 18 are associated with cervical cancer. Here, based on the high structural similarity of L1 surface loops within a group of phylogenetically close HPV types, we design a triple-type chimera of HPV33/58/52 using loop swapping. The chimeric VLPs elicit neutralization titers comparable with a mix of the three wild-type VLPs both in mice and non-human primates. This engineered region of the chimeric protein recapitulates the conformational contours of the antigenic surfaces of the parental-type proteins, offering a basis for this high immunity. Our stratagem is equally successful in developing other triplet-type chimeras (HPV16/35/31, HPV56/66/53, HPV39/68/70, HPV18/45/59), paving the way for the development of an improved HPV prophylactic vaccine against all carcinogenic HPV strains. This technique may also be extrapolated to other microbes.
History
DepositionSep 25, 2018-
Header (metadata) releaseNov 14, 2018-
Map releaseNov 14, 2018-
UpdateMay 29, 2019-
Current statusMay 29, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 12.5086
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 12.5086
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9665.png

Downloads & links

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Map

FileDownload / File: emd_9665.map.gz / Format: CCP4 / Size: 2.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 861 pix.
= 971.208 Å		1.13 Å/pix.
x 861 pix.
= 971.208 Å		1.13 Å/pix.
x 861 pix.
= 971.208 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: 12.508599999999999 / Movie #1: 12.5086
Minimum - Maximum-51.289363999999999 - 59.170074
Average (Standard dev.)0.028689172 (±6.253323)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-430-430-430
Dimensions861861861
Spacing861861861
CellA=B=C: 971.208 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1281.1281.128
M x/y/z861861861
origin x/y/z0.0000.0000.000
length x/y/z971.208971.208971.208
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-430-430-430
NC/NR/NS861861861
D min/max/mean-51.28959.1700.029

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Supplemental data

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Sample components

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Entire : Human papillomavirus type 33

EntireName: Human papillomavirus type 33
Components
  • Virus: Human papillomavirus type 33

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Supramolecule #1: Human papillomavirus type 33

SupramoleculeName: Human papillomavirus type 33 / type: virus / ID: 1 / Parent: 0
Details: VLP generated by recombinantly expressed; Fab Fragment generated by proteolytic cleavage of IgG antibody;
NCBI-ID: 10586 / Sci species name: Human papillomavirus type 33 / 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 II (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: 12.3 Å / Resolution method: OTHER / Details: FSC 0.3 cut-off / Number images used: 753
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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