[English] 日本語
Yorodumi
- EMDB-14179: HeLa cell expressing NSP3, NSP4 and NSP6 of SARS-CoV-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14179
TitleHeLa cell expressing NSP3, NSP4 and NSP6 of SARS-CoV-2
Map dataEM tomography of HeLa cell expressing NSP3, NSP4 and NSP6 of SARS-CoV-2
Sample
  • Cell: Thick section of plastic embedded HeLa cells co-expressing SARS-CoV-2 NSP3/4/6.
Biological speciesHomo sapiens (human)
Methodelectron tomography / negative staining
AuthorsPolishchuk R
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2022
Title: The role of NSP6 in the biogenesis of the SARS-CoV-2 replication organelle.
Authors: Simona Ricciardi / Andrea Maria Guarino / Laura Giaquinto / Elena V Polishchuk / Michele Santoro / Giuseppe Di Tullio / Cathal Wilson / Francesco Panariello / Vinicius C Soares / Suelen S G ...Authors: Simona Ricciardi / Andrea Maria Guarino / Laura Giaquinto / Elena V Polishchuk / Michele Santoro / Giuseppe Di Tullio / Cathal Wilson / Francesco Panariello / Vinicius C Soares / Suelen S G Dias / Julia C Santos / Thiago M L Souza / Giovanna Fusco / Maurizio Viscardi / Sergio Brandi / Patrícia T Bozza / Roman S Polishchuk / Rossella Venditti / Maria Antonietta De Matteis /
Abstract: SARS-CoV-2, like other coronaviruses, builds a membrane-bound replication organelle to enable RNA replication. The SARS-CoV-2 replication organelle is composed of double-membrane vesicles (DMVs) that ...SARS-CoV-2, like other coronaviruses, builds a membrane-bound replication organelle to enable RNA replication. The SARS-CoV-2 replication organelle is composed of double-membrane vesicles (DMVs) that are tethered to the endoplasmic reticulum (ER) by thin membrane connectors, but the viral proteins and the host factors involved remain unknown. Here we identify the viral non-structural proteins (NSPs) that generate the SARS-CoV-2 replication organelle. NSP3 and NSP4 generate the DMVs, whereas NSP6, through oligomerization and an amphipathic helix, zippers ER membranes and establishes the connectors. The NSP6(ΔSGF) mutant, which arose independently in the Alpha, Beta, Gamma, Eta, Iota and Lambda variants of SARS-CoV-2, behaves as a gain-of-function mutant with a higher ER-zippering activity. We identified three main roles for NSP6: first, to act as a filter in communication between the replication organelle and the ER, by allowing lipid flow but restricting the access of ER luminal proteins to the DMVs; second, to position and organize DMV clusters; and third, to mediate contact with lipid droplets (LDs) through the LD-tethering complex DFCP1-RAB18. NSP6 thus acts as an organizer of DMV clusters and can provide a selective means of refurbishing them with LD-derived lipids. Notably, both properly formed NSP6 connectors and LDs are required for the replication of SARS-CoV-2. Our findings provide insight into the biological activity of NSP6 of SARS-CoV-2 and of other coronaviruses, and have the potential to fuel the search for broad antiviral agents.
History
DepositionJan 21, 2022-
Header (metadata) releaseFeb 9, 2022-
Map releaseFeb 9, 2022-
UpdateJul 6, 2022-
Current statusJul 6, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Supplemental images

emd_14179.png

Downloads & links

-
Map

FileDownload / File: emd_14179.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationEM tomography of HeLa cell expressing NSP3, NSP4 and NSP6 of SARS-CoV-2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.91 Å/pix.
x 2048 pix.
= 14147.584 Å		6.91 Å/pix.
x 156 pix.
= 1077.648 Å		6.91 Å/pix.
x 2048 pix.
= 14147.584 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: 6.908 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-5358.0 - 3973.0
Average (Standard dev.)278.88428 (±205.02829)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin7800
Dimensions15620482048
Spacing20481562048
CellA: 14147.584 Å / B: 1077.648 Å / C: 14147.584 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z6.9086.9086.908
M x/y/z20481562048
origin x/y/z0.0000.0000.000
length x/y/z14147.5841077.64814147.584
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS0780
NC/NR/NS20481562048
D min/max/mean-5358.0003973.000278.884

-
Supplemental data

-
Sample components

-
Entire : Thick section of plastic embedded HeLa cells co-expressing SARS-C...

EntireName: Thick section of plastic embedded HeLa cells co-expressing SARS-CoV-2 NSP3/4/6.
Components
  • Cell: Thick section of plastic embedded HeLa cells co-expressing SARS-CoV-2 NSP3/4/6.

-
Supramolecule #1: Thick section of plastic embedded HeLa cells co-expressing SARS-C...

SupramoleculeName: Thick section of plastic embedded HeLa cells co-expressing SARS-CoV-2 NSP3/4/6.
type: cell / ID: 1 / Parent: 0
Details: The tomogram shows double membrane vesicles connected to zippered ER domain.
Source (natural)Organism: Homo sapiens (human)

-
Experimental details

-
Structure determination

Methodnegative staining
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.2
StainingType: POSITIVE / Material: Uranyl Acetate, OsO4
Sugar embeddingMaterial: Epon
DetailsEpon embedded pellet from cultured HeLa cells
SectioningUltramicrotomy - Instrument: Leica EM UC7 / Ultramicrotomy - Temperature: 20 K / Ultramicrotomy - Final thickness: 250 nm
Fiducial markerManufacturer: Aurion / Diameter: 10 nm

-
Electron microscopy

MicroscopeFEI TECNAI 12
Image recordingFilm or detector model: OTHER / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FISCHIONE 2550

-
Image processing

DetailsIMOD
Final reconstructionNumber images used: 131

+
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