[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleReceptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion.
Journal, issue, pagesNature, Vol. 588, Issue 7837, Page 327-330, Year 2020
Publish dateSep 17, 2020
AuthorsDonald J Benton / Antoni G Wrobel / Pengqi Xu / Chloë Roustan / Stephen R Martin / Peter B Rosenthal / John J Skehel / Steven J Gamblin /
PubMed AbstractInfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is initiated by virus binding to the ACE2 cell-surface receptors, followed by fusion of the virus and cell membranes to ...Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is initiated by virus binding to the ACE2 cell-surface receptors, followed by fusion of the virus and cell membranes to release the virus genome into the cell. Both receptor binding and membrane fusion activities are mediated by the virus spike glycoprotein. As with other class-I membrane-fusion proteins, the spike protein is post-translationally cleaved, in this case by furin, into the S1 and S2 components that remain associated after cleavage. Fusion activation after receptor binding is proposed to involve the exposure of a second proteolytic site (S2'), cleavage of which is required for the release of the fusion peptide. Here we analyse the binding of ACE2 to the furin-cleaved form of the SARS-CoV-2 spike protein using cryo-electron microscopy. We classify ten different molecular species, including the unbound, closed spike trimer, the fully open ACE2-bound trimer and dissociated monomeric S1 bound to ACE2. The ten structures describe ACE2-binding events that destabilize the spike trimer, progressively opening up, and out, the individual S1 components. The opening process reduces S1 contacts and unshields the trimeric S2 core, priming the protein for fusion activation and dissociation of ACE2-bound S1 monomers. The structures also reveal refolding of an S1 subdomain after ACE2 binding that disrupts interactions with S2, which involves Asp614 and leads to the destabilization of the structure of S2 proximal to the secondary (S2') cleavage site.
External linksNature / PubMed:32942285 / PubMed Central
MethodsEM (single particle)
Resolution3.6 - 5.9 Å
Structure data

EMDB-11681, PDB-7a91:
Dissociated S1 domain of SARS-CoV-2 Spike bound to ACE2 (Non-Uniform Refinement)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-11682, PDB-7a92:
Dissociated S1 domain of SARS-CoV-2 Spike bound to ACE2 (Unmasked Refinement)
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-11683, PDB-7a93:
SARS-CoV-2 Spike Glycoprotein with 2 RBDs Erect
Method: EM (single particle) / Resolution: 5.9 Å

EMDB-11684, PDB-7a94:
SARS-CoV-2 Spike Glycoprotein with 1 ACE2 Bound
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-11685, PDB-7a95:
SARS-CoV-2 Spike Glycoprotein with 1 ACE2 Bound and 1 RBD Erect in Clockwise Direction
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-11686, PDB-7a96:
SARS-CoV-2 Spike Glycoprotein with 1 ACE2 Bound and 1 RBD Erect in Anticlockwise Direction
Method: EM (single particle) / Resolution: 4.8 Å

EMDB-11687, PDB-7a97:
SARS-CoV-2 Spike Glycoprotein with 2 ACE2 Bound
Method: EM (single particle) / Resolution: 4.4 Å

EMDB-11688, PDB-7a98:
SARS-CoV-2 Spike Glycoprotein with 3 ACE2 Bound
Method: EM (single particle) / Resolution: 5.4 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

ChemComp-ZN:
Unknown entry

Source
  • homo sapiens (human)
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Spike / Virus Glycoprotein / Coronavirus / ACE2

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more