[English] 日本語
Yorodumi
- EMDB-13856: Tomogram of respiratory syncytial virus filamentous virion -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13856
TitleTomogram of respiratory syncytial virus filamentous virion
Map dataRepresentative tomogram of filamentous respiratory syncytial virus
Sample
  • Virus: Respiratory syncytial virus A2
    • Organelle or cellular component: Budding RSV Virion
KeywordsVirion / VIRUS
Biological speciesRespiratory syncytial virus A2
Methodelectron tomography / cryo EM
AuthorsConley MJ / Vijayakrishnan S / Bhella D
Funding support United Kingdom, 5 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_12014/7 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/M000451/1 United Kingdom
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI113321 United Kingdom
Wellcome Trust102463/Z/13/Z United Kingdom
Wellcome Trust099786/Z/12/Z United Kingdom
CitationJournal: EMBO J / Year: 2022
Title: Helical ordering of envelope-associated proteins and glycoproteins in respiratory syncytial virus.
Authors: Michaela J Conley / Judith M Short / Andrew M Burns / James Streetley / Joshua Hutchings / Saskia E Bakker / B Joanne Power / Hussain Jaffery / Joanne Haney / Giulia Zanetti / Pablo R Murcia ...Authors: Michaela J Conley / Judith M Short / Andrew M Burns / James Streetley / Joshua Hutchings / Saskia E Bakker / B Joanne Power / Hussain Jaffery / Joanne Haney / Giulia Zanetti / Pablo R Murcia / Murray Stewart / Rachel Fearns / Swetha Vijayakrishnan / David Bhella /
Abstract: Human respiratory syncytial virus (RSV) causes severe respiratory illness in children and the elderly. Here, using cryogenic electron microscopy and tomography combined with computational image ...Human respiratory syncytial virus (RSV) causes severe respiratory illness in children and the elderly. Here, using cryogenic electron microscopy and tomography combined with computational image analysis and three-dimensional reconstruction, we show that there is extensive helical ordering of the envelope-associated proteins and glycoproteins of RSV filamentous virions. We calculated a 16 Å resolution sub-tomogram average of the matrix protein (M) layer that forms an endoskeleton below the viral envelope. These data define a helical lattice of M-dimers, showing how M is oriented relative to the viral envelope. Glycoproteins that stud the viral envelope were also found to be helically ordered, a property that was coordinated by the M-layer. Furthermore, envelope glycoproteins clustered in pairs, a feature that may have implications for the conformation of fusion (F) glycoprotein epitopes that are the principal target for vaccine and monoclonal antibody development. We also report the presence, in authentic virus infections, of N-RNA rings packaged within RSV virions. These data provide molecular insight into the organisation of the virion and the mechanism of its assembly.
History
DepositionNov 5, 2021-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_13856.png

Downloads & links

-
Map

FileDownload / File: emd_13856.map.gz / Format: CCP4 / Size: 56 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRepresentative tomogram of filamentous respiratory syncytial virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.79 Å/pix.
x 3710 pix.
= 6640.9 Å		1.79 Å/pix.
x 1056 pix.
= 1890.24 Å		1.79 Å/pix.
x 3838 pix.
= 6870.02 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.79 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-169.063520000000011 - 162.010559999999998
Average (Standard dev.)0.0028832706 (±22.863993000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions105638383710
Spacing383810563710
CellA: 6870.02 Å / B: 1890.24 Å / C: 6640.9 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Respiratory syncytial virus A2

EntireName: Respiratory syncytial virus A2
Components
  • Virus: Respiratory syncytial virus A2
    • Organelle or cellular component: Budding RSV Virion

-
Supramolecule #1: Respiratory syncytial virus A2

SupramoleculeName: Respiratory syncytial virus A2 / type: virus / ID: 1 / Parent: 0
Details: Sub tomogram averaging was performed focusing on the envelope of filamentous virions propagated directly on the cryo-EM grid.
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

-
Supramolecule #2: Budding RSV Virion

SupramoleculeName: Budding RSV Virion / type: organelle_or_cellular_component / ID: 2 / Parent: 1
Source (natural)Organism: Respiratory syncytial virus A2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
Details: Grids were sterilised in EtOH and pretreated with laminin.
VitrificationCryogen name: ETHANE
DetailsVirions were propagated in A549 cells, grown on gold quantifoil cryo-EM grids that had been pre-treated with laminin.
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: BBI / Diameter: 5 nm

-
Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 2.0 e/Å2
Details: Data collected at the UK electron bioimaging centre at Diamond Light Source (eBIC) on a Thermo-Fisher Scientific Titan Krios microscope equipped with a Gatan BioQuantum K2 energy filtered ...Details: Data collected at the UK electron bioimaging centre at Diamond Light Source (eBIC) on a Thermo-Fisher Scientific Titan Krios microscope equipped with a Gatan BioQuantum K2 energy filtered direct detection camera. Dose-symmetric tilt-series collection was performed using SerialEM. Energy-filtered images were collected with a slit-width of 20eV and an applied defocus of between -2 and -4.5 microns. One second exposures were recorded with an electron exposure of 2 electrons/A2, partitioned over five movie frames. A total of 41 images were recorded per tilt-series at 3 degree intervals from -60 to +60, thus a total exposure of 82 electrons/A2 was applied per tilt-series. Tilt-series were recorded at a nominal column magnification of 81k corresponding to a calibrated pixel size of 1.79 A at the specimen scale.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 41
DetailsIndividual movies were corrected for drift and beam induced motion using MotionCor2. Motion corrected images were then compiled into an angle ordered stack file using a perl script to extract the correct files and tilt angles from the SerialEM metadata files (mdoc), creating the final tilt-series using the IMOD command new-stack. Tilt-series alignment and reconstruction by weighted back projection was then accomplished using the IMOD package

+
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