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- EMDB-30415: The cryo-EM structure of human papillomavirus type 16 pesudovirus... -

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Basic information

Entry
Database: EMDB / ID: EMD-30415
TitleThe cryo-EM structure of human papillomavirus type 16 pesudovirus in complex with Fab H16.001
Map dataThe cryo-EM structure of human papillomavirus type 58 pseudovirus complexed with H16.001 Fab
Sample
  • Virus: Human papillomavirus type 16
Biological speciesHuman papillomavirus type 16
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsHe MZ / Li SW
CitationJournal: NPJ Vaccines / Year: 2020
Title: Structural characterization of a neutralizing mAb H16.001, a potent candidate for a common potency assay for various HPV16 VLPs.
Authors: Weijin Huang / Maozhou He / Tingting Ning / Jianhui Nie / Feng Zhang / Qingbing Zheng / Rui Zhang / Ying Xu / Ying Gu / Shaowei Li / Youchun Wang /
Abstract: With more human papillomavirus (HPV) virus-like particle (VLP) vaccines to hit the market in future, a monoclonal antibody (mAb) with preferably comparable reactivity against vaccines from different ...With more human papillomavirus (HPV) virus-like particle (VLP) vaccines to hit the market in future, a monoclonal antibody (mAb) with preferably comparable reactivity against vaccines from different expression systems and bioprocesses is urgently needed for the potency characterization. Among all mAbs against HPV16 collected, rabbit mAb H16.001 is potently neutralizing with the highest affinity, recognizes an immune-dominant epitope, and can comparably react with HPV16 vaccines from various sources. Cryo-electron microscopic (cryo-EM) structure demonstrated that 360 H16.001 Fabs could bind to HPV16 capsid in preferable binding manner without steric hindrance between neighboring Fabs, potentially supporting its identification for VLP structural integrity and utility in monitoring VLP structural probity. This structural analysis indicated that mAb H16.001 afforded unbiased potency characterization for various HPV16 vaccines and was potential for use in vaccine regulation practice. This study also showed a model process for selecting suitable mAbs for potency assays of other vaccines.
History
DepositionJul 29, 2020-
Header (metadata) releaseSep 2, 2020-
Map releaseSep 2, 2020-
UpdateSep 2, 2020-
Current statusSep 2, 2020Processing 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_30415.png

Downloads & links

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Map

FileDownload / File: emd_30415.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe cryo-EM structure of human papillomavirus type 58 pseudovirus complexed with H16.001 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 768 pix.
= 866.304 Å		1.13 Å/pix.
x 768 pix.
= 866.304 Å		1.13 Å/pix.
x 768 pix.
= 866.304 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: 5 / Movie #1: 5
Minimum - Maximum-11.069445 - 17.858284
Average (Standard dev.)0.024540057 (±1.5274532)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 866.304 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1281.1281.128
M x/y/z768768768
origin x/y/z0.0000.0000.000
length x/y/z866.304866.304866.304
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS768768768
D min/max/mean-11.06917.8580.025

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Supplemental data

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Sample components

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Entire : Human papillomavirus type 16

EntireName: Human papillomavirus type 16
Components
  • Virus: Human papillomavirus type 16

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Supramolecule #1: Human papillomavirus type 16

SupramoleculeName: Human papillomavirus type 16 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 333760 / Sci species name: Human papillomavirus type 16 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host systemOrganism: Homo sapiens (human)

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / 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: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9162
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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