[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

TitleCharacterization and structural basis of a lethal mouse-adapted SARS-CoV-2.
Journal, issue, pagesNat Commun, Vol. 12, Issue 1, Page 5654, Year 2021
Publish dateSep 27, 2021
AuthorsShihui Sun / Hongjing Gu / Lei Cao / Qi Chen / Qing Ye / Guan Yang / Rui-Ting Li / Hang Fan / Yong-Qiang Deng / Xiaopeng Song / Yini Qi / Min Li / Jun Lan / Rui Feng / Yan Guo / Na Zhu / Si Qin / Lei Wang / Yi-Fei Zhang / Chao Zhou / Lingna Zhao / Yuehong Chen / Meng Shen / Yujun Cui / Xiao Yang / Xinquan Wang / Wenjie Tan / Hui Wang / Xiangxi Wang / Cheng-Feng Qin /
PubMed AbstractThere is an urgent need for animal models to study SARS-CoV-2 pathogenicity. Here, we generate and characterize a novel mouse-adapted SARS-CoV-2 strain, MASCp36, that causes severe respiratory ...There is an urgent need for animal models to study SARS-CoV-2 pathogenicity. Here, we generate and characterize a novel mouse-adapted SARS-CoV-2 strain, MASCp36, that causes severe respiratory symptoms, and mortality. Our model exhibits age- and gender-related mortality akin to severe COVID-19. Deep sequencing identified three amino acid substitutions, N501Y, Q493H, and K417N, at the receptor binding domain (RBD) of MASCp36, during in vivo passaging. All three RBD mutations significantly enhance binding affinity to its endogenous receptor, ACE2. Cryo-electron microscopy analysis of human ACE2 (hACE2), or mouse ACE2 (mACE2), in complex with the RBD of MASCp36, at 3.1 to 3.7 Å resolution, reveals the molecular basis for the receptor-binding switch. N501Y and Q493H enhance the binding affinity to hACE2, whereas triple mutations at N501Y/Q493H/K417N decrease affinity and reduce infectivity of MASCp36. Our study provides a platform for studying SARS-CoV-2 pathogenesis, and unveils the molecular mechanism for its rapid adaptation and evolution.
External linksNat Commun / PubMed:34580297 / PubMed Central
MethodsEM (single particle)
Resolution3.12 - 3.72 Å
Structure data

31542

7fdg

EMDB-31542, PDB-7fdg:
SARS-COV-2 Spike RBDMACSp6 binding to hACE2
Method: EM (single particle) / Resolution: 3.69 Å

31543

7fdh

EMDB-31543, PDB-7fdh:
SARS-COV-2 Spike RBDMACSp25 binding to hACE2
Method: EM (single particle) / Resolution: 3.72 Å

31544

7fdi

EMDB-31544, PDB-7fdi:
SARS-COV-2 Spike RBDMACSp36 binding to hACE2
Method: EM (single particle) / Resolution: 3.12 Å

31546

7fdk

EMDB-31546, PDB-7fdk:
SARS-COV-2 Spike RBDMACSp36 binding to mACE2
Method: EM (single particle) / Resolution: 3.69 Å

Chemicals

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

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
  • mus musculus (house mouse)
KeywordsVIRAL PROTEIN / SARS-COV-2 Spike / mouse-adapted / RBD / ACE2 / VIRUS PROTEIN / VIRUS / hACE2 / mACE2

+
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