[English] 日本語
Yorodumi
- EMDB-15579: Bunyamwera Virus Gn/Gc Glycoprotein pH 6.3/K+ Treated -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15579
TitleBunyamwera Virus Gn/Gc Glycoprotein pH 6.3/K+ Treated
Map data
Sample
  • Virus: Bunyamwera virus
KeywordsGlycoprotein / fusion protein / orthobunyavirus / primed / VIRAL PROTEIN
Biological speciesBunyamwera virus
Methodsubtomogram averaging / cryo EM / Resolution: 16.0 Å
AuthorsHover S / Fontana J
Funding support United Kingdom, France, 5 items
OrganizationGrant numberCountry
Wellcome TrustSBF002/1029 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/T016159/1 United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
Wellcome Trust090932/Z/09/Z United Kingdom
Human Frontier Science Program (HFSP)RGP0040/2019 France
CitationJournal: Nat Commun / Year: 2023
Title: Organisation of the orthobunyavirus tripodal spike and the structural changes induced by low pH and K during entry.
Authors: Samantha Hover / Frank W Charlton / Jan Hellert / Jessica J Swanson / Jamel Mankouri / John N Barr / Juan Fontana /
Abstract: Following endocytosis, enveloped viruses employ the changing environment of maturing endosomes as cues to promote endosomal escape, a process often mediated by viral glycoproteins. We previously ...Following endocytosis, enveloped viruses employ the changing environment of maturing endosomes as cues to promote endosomal escape, a process often mediated by viral glycoproteins. We previously showed that both high [K] and low pH promote entry of Bunyamwera virus (BUNV), the prototypical bunyavirus. Here, we use sub-tomogram averaging and AlphaFold, to generate a pseudo-atomic model of the whole BUNV glycoprotein envelope. We unambiguously locate the Gc fusion domain and its chaperone Gn within the floor domain of the spike. Furthermore, viral incubation at low pH and high [K], reminiscent of endocytic conditions, results in a dramatic rearrangement of the BUNV envelope. Structural and biochemical assays indicate that pH 6.3/K in the absence of a target membrane elicits a fusion-capable triggered intermediate state of BUNV GPs; but the same conditions induce fusion when target membranes are present. Taken together, we provide mechanistic understanding of the requirements for bunyavirus entry.
History
DepositionAug 11, 2022-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateOct 4, 2023-
Current statusOct 4, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15579.png

Downloads & links

-
Map

FileDownload / File: emd_15579.map.gz / Format: CCP4 / Size: 262.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.44 Å/pix.
x 40 pix.
= 217.6 Å		5.44 Å/pix.
x 42 pix.
= 228.48 Å		5.44 Å/pix.
x 40 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 5.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 350.0
Minimum - Maximum-1000.810899999999947 - 2307.800299999999879
Average (Standard dev.)-14.0878725 (±291.038000000000011)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions424040
Spacing404240
CellA: 217.6 Å / B: 228.48 Å / C: 217.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_15579_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_15579_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Bunyamwera virus

EntireName: Bunyamwera virus
Components
  • Virus: Bunyamwera virus

-
Supramolecule #1: Bunyamwera virus

SupramoleculeName: Bunyamwera virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 35304 / Sci species name: Bunyamwera virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferpH: 6.3
Component:
ConcentrationFormulaName
28.0 mMC8H19NO5Bis-Tris
128.0 mMKClPotassium Chloride
10.0 mMNaClSodium Chloride

Details: Virions were treated for 2 hrs in pH 6.3/K+ buffer, prior to vitrification
VitrificationCryogen name: ETHANE
DetailsVirions pH 6.3/K+ treated prior to vitrification

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 9987
ExtractionNumber tomograms: 14 / Number images used: 18312
Final 3D classificationNumber classes: 3
Details: Owing to heterogeneity and flexibility of the sample, particles separated into three classes using PEET programmes pca and clusterPca.
Final angle assignmentType: OTHER / Details: PEET software used - 3D reference matching
FSC plot (resolution estimation)

+
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