[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

TitleA coronavirus assembly inhibitor that targets the viral membrane protein.
Journal, issue, pagesNature, Vol. 640, Issue 8058, Page 514-523, Year 2025
Publish dateMar 26, 2025
AuthorsManon Laporte / Dirk Jochmans / Dorothée Bardiot / Lowiese Desmarets / Oliver J Debski-Antoniak / Giulia Mizzon / Rana Abdelnabi / Pieter Leyssen / Winston Chiu / Zhikuan Zhang / Norimichi Nomura / Sandro Boland / Umeharu Ohto / Yannick Stahl / Jurgen Wuyts / Steven De Jonghe / Annelies Stevaert / Martijn J van Hemert / Brenda W Bontes / Patrick Wanningen / G J Mirjam Groenewold / Aneta Zegar / Katarzyna Owczarek / Sanjata Joshi / Mohamed Koukni / Philippe Arzel / Hugo Klaassen / Jean-Christophe Vanherck / Ilse Vandecaetsbeek / Niels Cremers / Kim Donckers / Thibault Francken / Tina Van Buyten / Jasper Rymenants / Joost Schepers / Krzysztof Pyrc / Rolf Hilgenfeld / Jean Dubuisson / Berend-Jan Bosch / Frank Van Kuppeveld / Cecilia Eydoux / Etienne Decroly / Bruno Canard / Lieve Naesens / Birgit Weynand / Eric J Snijder / Sandrine Belouzard / Toshiyuki Shimizu / Ralf Bartenschlager / Daniel L Hurdiss / Arnaud Marchand / Patrick Chaltin / Johan Neyts /
PubMed AbstractThe coronavirus membrane protein (M) is the main organizer of coronavirus assembly. Here, we report on an M-targeting molecule, CIM-834, that blocks the assembly of SARS-CoV-2. CIM-834 was obtained ...The coronavirus membrane protein (M) is the main organizer of coronavirus assembly. Here, we report on an M-targeting molecule, CIM-834, that blocks the assembly of SARS-CoV-2. CIM-834 was obtained through high-throughput phenotypic antiviral screening followed by medicinal-chemistry efforts and target elucidation. CIM-834 inhibits the replication of SARS-CoV-2 (including a broad panel of variants) and SARS-CoV. In SCID mice and Syrian hamsters intranasally infected with SARS-CoV-2, oral treatment reduced lung viral titres to nearly undetectable levels, even (as shown in mice) when treatment was delayed until 24 h before the end point. Treatment of infected hamsters prevented transmission to untreated sentinels. Transmission electron microscopy studies show that virion assembly is completely absent in cells treated with CIM-834. Single-particle cryo-electron microscopy reveals that CIM-834 binds and stabilizes the M protein in its short form, thereby preventing the conformational switch to the long form, which is required for successful particle assembly. In conclusion, we have discovered a new druggable target in the replication cycle of coronaviruses and a small molecule that potently inhibits it.
External linksNature / PubMed:40140569 / PubMed Central
MethodsEM (single particle)
Resolution3.2 - 3.3 Å
Structure data

50034

9exa

EMDB-50034, PDB-9exa:
SARS-CoV-2 M protein dimer (short form) in complex with Fab-B and CIM-834
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-50035: SARS-CoV-2 M protein dimer (long form) in complex with Fab-E and incubated with CIM-834
Method: EM (single particle) / Resolution: 3.3 Å

Chemicals

PDB-1h7w:
Dihydropyrimidine dehydrogenase (DPD) from pig

Source
  • severe acute respiratory syndrome coronavirus 2
  • mus musculus (house mouse)
KeywordsVIRAL PROTEIN / Inhibitor / Complex / Membrane protein / Antibody

+
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