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- EMDB-5839: Characterization of Human Papilloma Virus Type 16 VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-5839
TitleCharacterization of Human Papilloma Virus Type 16 VLP
Map dataReconstruction of HPV Type 16 VLP
Sample
  • Sample: Human Papilloma Virus Type 16 VLP
  • Virus: Human papillomavirus
KeywordsHuman Papilloma Virus Type 16 VLP
Biological speciesHuman papillomavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 13.0 Å
AuthorsZhao Q / Potter CS / Carragher B / Lander G / Sworen J / Towne V / Abraham D / Duncan P / Washabaugh MW / Sitrin RD
CitationJournal: Hum Vaccin Immunother / Year: 2014
Title: Characterization of virus-like particles in GARDASIL® by cryo transmission electron microscopy.
Authors: Qinjian Zhao / Clinton S Potter / Bridget Carragher / Gabriel Lander / Jaime Sworen / Victoria Towne / Dicky Abraham / Paul Duncan / Michael W Washabaugh / Robert D Sitrin /
Abstract: Cryo-transmission electron microscopy (cryoTEM) is a powerful characterization method for assessing the structural properties of biopharmaceutical nanoparticles, including Virus Like Particle-based ...Cryo-transmission electron microscopy (cryoTEM) is a powerful characterization method for assessing the structural properties of biopharmaceutical nanoparticles, including Virus Like Particle-based vaccines. We demonstrate the method using the Human Papilloma Virus (HPV) VLPs in GARDASIL®. CryoTEM, coupled to automated data collection and analysis, was used to acquire images of the particles in their hydrated state, determine their morphological characteristics, and confirm the integrity of the particles when absorbed to aluminum adjuvant. In addition, we determined the three-dimensional structure of the VLPs, both alone and when interacting with neutralizing antibodies. Two modes of binding of two different neutralizing antibodies were apparent; for HPV type 11 saturated with H11.B2, 72 potential Fab binding sites were observed at the center of each capsomer, whereas for HPV 16 interacting with H16.V5, it appears that 60 pentamers (each neighboring 6 other pentamers) bind five Fabs per pentamer, for the total of 300 potential Fab binding sites per VLP.
History
DepositionDec 15, 2013-
Header (metadata) releaseMar 19, 2014-
Map releaseMar 19, 2014-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5839.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of HPV Type 16 VLP
Voxel sizeX=Y=Z: 3.26 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-4.48136425 - 5.85216093
Average (Standard dev.)0.02206318 (±0.89059055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-90-90-90
Dimensions180180180
Spacing180180180
CellA=B=C: 586.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.263.263.26
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z586.800586.800586.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-90-90-90
NC/NR/NS180180180
D min/max/mean-4.4815.8520.022

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Supplemental data

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Sample components

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Entire : Human Papilloma Virus Type 16 VLP

EntireName: Human Papilloma Virus Type 16 VLP
Components
  • Sample: Human Papilloma Virus Type 16 VLP
  • Virus: Human papillomavirus

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Supramolecule #1000: Human Papilloma Virus Type 16 VLP

SupramoleculeName: Human Papilloma Virus Type 16 VLP / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Human papillomavirus

SupramoleculeName: Human papillomavirus / type: virus / ID: 1 / NCBI-ID: 10566 / Sci species name: Human papillomavirus / Database: NCBI / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes / Sci species serotype: Type 16
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES

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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

VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
DateNov 29, 2006
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: OTHER / Software - Name: EMAN / Number images used: 5135

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