[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 structural basis of raccoon dog ACE2 binding to SARS-CoV-2 prototype and its variants.
Journal, issue, pagesPLoS Pathog, Vol. 20, Issue 12, Page e1012713, Year 2024
Publish dateDec 5, 2024
AuthorsChunliang Luo / Linjie Li / Yuhang Gu / Hangchuan Zhang / Zepeng Xu / Junqing Sun / Kaiyuan Shi / Sufang Ma / Wen-Xia Tian / Kefang Liu / George F Gao /
PubMed AbstractRaccoon dog was proposed as a potential host of SARS-CoV-2, but no evidence support such a notion. In our study, we investigated the binding affinities of raccoon dog ACE2 (rdACE2) to the spike (S) ...Raccoon dog was proposed as a potential host of SARS-CoV-2, but no evidence support such a notion. In our study, we investigated the binding affinities of raccoon dog ACE2 (rdACE2) to the spike (S) protein receptor binding domain (RBD) of SARS-CoV-2 prototype (PT) and its variants. It revealed that the binding affinities of RBD from SARS-CoV-2 variants were generally lower than that of the PT RBD. Through structural and functional analyses, we found amino acids H34 and M82 play pivotal roles in maintaining the binding affinity of ACE2 to different SARS-CoV-2 sub-variants. These results suggest that raccoon dogs exhibit lower susceptibility to SARS-CoV-2 compared to those animal species with a high prevalence of SARS-CoV-2 transmission.
External linksPLoS Pathog / PubMed:39637248 / PubMed Central
MethodsEM (single particle)
Resolution2.52 - 3.16 Å
Structure data

39208

8yf2

EMDB-39208, PDB-8yf2:
Cryo-EM structure of SARS-CoV-2 prototype RBD in complex with raccoon dog ACE2 (local refinement)
Method: EM (single particle) / Resolution: 2.64 Å

EMDB-39209: Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with raccoon dog ACE2
Method: EM (single particle) / Resolution: 2.52 Å

EMDB-39224: Cryo-EM map of SARS-CoV-2 alpha variant spike protein in complex with raccoon dog ACE2
Method: EM (single particle) / Resolution: 2.86 Å

39229

8yft

EMDB-39229, PDB-8yft:
Cryo-EM structure of SARS-CoV-2 alpha variant spike protein in complex with raccoon dog ACE2 (local refinement)
Method: EM (single particle) / Resolution: 3.16 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

Source
  • severe acute respiratory syndrome coronavirus 2
  • nyctereutes procyonoides (raccoon dog)
KeywordsVIRAL PROTEIN/HYDROLASE / SARS-CoV-2 / rototype RBD / raccoon dog / ACE2 / VIRAL PROTEIN-HYDROLASE Complex / alpha / RBD

+
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