[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

TitleCX1/BtSY2 and BANAL-20-52 exhibit broader receptor binding and higher affinities to multiple animal ACE2 orthologs than SARS-CoV-2 prototype.
Journal, issue, pagesJ Virol, Vol. 99, Issue 8, Page e0028325, Year 2025
Publish dateAug 19, 2025
AuthorsZepeng Xu / Linjie Li / Yuhang Gu / Dedong Li / Jianxun Qi / Kefang Liu / Chu-Xia Deng / George Fu Gao /
PubMed AbstractAnimal coronaviruses (CoVs) CX1 (formerly named BtSY2) and BANAL-20-52 are phylogenetically closely related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and CX1 is the first ...Animal coronaviruses (CoVs) CX1 (formerly named BtSY2) and BANAL-20-52 are phylogenetically closely related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and CX1 is the first observed animal betaCoV carrying naturally occurring Y501 in its receptor-binding domain (RBD) of the spike (S) protein, a residue related to human adaptation and broader host range. We evaluated the ACE2 usage of CX1 and BANAL-20-52 and observed broader receptor binding spectra and higher affinities to most of the tested animal ACE2 orthologs than the SARS-CoV-2 prototype. Determination of the cryo-EM structures of their S proteins and RBD/hACE2 complexes reveals that Y501 is inter-replaceable with H498 substitution while synergetic with R498 for human ACE2 binding. These results provide further structural insights into SARS-CoV-2 receptor recognition and address the importance of surveillance on potential emerging CoVs.IMPORTANCESince the outbreak of COVID-19, forewarning and prevention of the next pandemic have been widely discussed. Coronaviruses (CoVs) CX1 (formerly named BtSY2) and BANAL-20-52 are phylogenetically closely related to SARS-CoV-2. Particularly, CX1 is the first SARS-CoV-2-related CoV containing Y501 in its receptor-binding domain (RBD) of the spike (S) protein. This study evaluated the interspecies transmission potential of the two CoVs and structurally elucidated the interplay between two RBD residues 498 and 501 on ACE2 binding, further highlighting the importance of surveillance on zoonotic CoVs.
External linksJ Virol / PubMed:40637421 / PubMed Central
MethodsEM (single particle)
Resolution2.5 - 3.04 Å
Structure data

38773

8xyh

EMDB-38773, PDB-8xyh:
Cryo-EM structure of BANAL-20-52 spike protein (6P)
Method: EM (single particle) / Resolution: 2.5 Å

38778

8xym

EMDB-38778, PDB-8xym:
Cryo-EM structure of CX1 spike protein (6P)
Method: EM (single particle) / Resolution: 2.74 Å

38779

8xyo

EMDB-38779, PDB-8xyo:
Cryo-EM structure of CX1 receptor binding domain in complex with human ACE2
Method: EM (single particle) / Resolution: 3.04 Å

Chemicals

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

ChemComp-EIC:
LINOLEIC ACID

ChemComp-ZN:
Unknown entry

Source
  • coronavirinae (virus)
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
KeywordsVIRAL PROTEIN / BANAL-20-52 / spike protein / CX1 / HYDROLASE/VIRAL PROTEIN / receptor binding domain / human ACE2 / HYDROLASE-VIRAL PROTEIN complex

+
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