[English] 日本語
Yorodumi
- EMDB-5838: Characterization of Human Papilloma Virus Type 11 VLP decorated w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5838
TitleCharacterization of Human Papilloma Virus Type 11 VLP decorated with antibody fragment H11.B2 B2
Map dataReconstruction of HPV Type 11 VLP + H11.B2 B2 Fab
Sample
  • Sample: Human Papilloma Virus Type 11 VLP decorated with antibody fragment H11.B2
  • Virus: Human papillomavirus
  • Protein or peptide: H11.B2 Fab
KeywordsHuman Papilloma Virus VLP
Biological speciesunidentified (others) / Human papillomavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 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

-
Structure visualization

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

emd_5838.png

Downloads & links

-
Map

FileDownload / File: emd_5838.map.gz / Format: CCP4 / Size: 41.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of HPV Type 11 VLP + H11.B2 B2 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.26 Å/pix.
x 224 pix.
= 730.24 Å		3.26 Å/pix.
x 224 pix.
= 730.24 Å		3.26 Å/pix.
x 224 pix.
= 730.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.26 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-3.59366655 - 5.23554087
Average (Standard dev.)0.0 (±0.95697534)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-112-112-112
Dimensions224224224
Spacing224224224
CellA=B=C: 730.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.263.263.26
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z730.240730.240730.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-112-112-112
NC/NR/NS224224224
D min/max/mean-3.5945.2360.000

-
Supplemental data

-
Sample components

-
Entire : Human Papilloma Virus Type 11 VLP decorated with antibody fragmen...

EntireName: Human Papilloma Virus Type 11 VLP decorated with antibody fragment H11.B2
Components
  • Sample: Human Papilloma Virus Type 11 VLP decorated with antibody fragment H11.B2
  • Virus: Human papillomavirus
  • Protein or peptide: H11.B2 Fab

-
Supramolecule #1000: Human Papilloma Virus Type 11 VLP decorated with antibody fragmen...

SupramoleculeName: Human Papilloma Virus Type 11 VLP decorated with antibody fragment H11.B2
type: sample / ID: 1000 / Number unique components: 2

-
Supramolecule #1: Human papillomavirus

SupramoleculeName: Human papillomavirus / type: virus / ID: 1
Details: VLP bound with Type 11 VLP dh antibody fragment H11.B2
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 11
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES

-
Macromolecule #1: H11.B2 Fab

MacromoleculeName: H11.B2 Fab / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: unidentified (others)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK II

-
Electron microscopy

MicroscopeFEI TECNAI F20
DateOct 11, 2006
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Software - Name: EMAN / Number images used: 6209

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more