[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

TitleDevelopment of an ultrahigh affinity, trimeric ACE2 biologic as a universal SARS-CoV-2 antagonist.
Journal, issue, pagesCommun Biol, Vol. 8, Issue 1, Page 1428, Year 2025
Publish dateOct 6, 2025
AuthorsJuliet Gonzales / Tynan Young / Hyeran Choi / Miso Park / Yead Jewel / Chengcheng Fan / Rahul Purohit / Pamela J Bjorkman / John C Williams /
PubMed AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, utilizes membrane-bound, angiotensin-converting enzyme II (ACE2) for internalization and infection. ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, utilizes membrane-bound, angiotensin-converting enzyme II (ACE2) for internalization and infection. We describe the development of a biologic that takes advantage of the proximity of the N-terminus of bound ACE2 to the three-fold symmetry axis of the spike protein to create an ultrapotent, trivalent ACE2 entry antagonist. Distinct disulfide bonds were added to enhance serum stability and a single point mutation was introduced to eliminate enzymatic activity. Through surface plasmon resonance, pseudovirus neutralization assays, and single-particle cryo-electron microscopy, we show this antagonist binds to and inhibits SARS-CoV-2 variants. We further show the antagonist binds to and inhibits a 2003 SARS-CoV-1 strain. Collectively, structural insight has allowed us to design a universal trivalent antagonist against all variants of SARS-CoV-2 tested, suggesting it will be active against the emergence of future mutants.
External linksCommun Biol / PubMed:41053501 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.4 - 3.73 Å
Structure data

44724

9bnd

EMDB-44724, PDB-9bnd:
SARS-CoV-2 spike HexaPro protein in complex with T0A trimeric antagonist
Method: EM (single particle) / Resolution: 3.19 Å

44725

9bne

EMDB-44725, PDB-9bne:
SARS-CoV-2 spike HexaPro protein in complex with T3A trimeric antagonist
Method: EM (single particle) / Resolution: 3.43 Å

44726

9bnf

EMDB-44726, PDB-9bnf:
SARS-CoV-2 spike HexaPro protein in complex with T5A trimeric antagonist
Method: EM (single particle) / Resolution: 3.33 Å

44727

9bng

EMDB-44727, PDB-9bng:
SARS-CoV-2 spike HexaPro protein in complex with T18A trimeric antagonist
Method: EM (single particle) / Resolution: 3.73 Å

PDB-9bnb:
Collagen XVIII trimerization domain with introduced inter-chain disulfide bond, G(-1)C-L5C
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-9bnc:
Collagen XVIII trimerization domain with introduced inter-chain disulfide bond, E31C-V37C
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

Chemicals

ChemComp-HOH:
WATER

ChemComp-SO4:
SULFATE ION

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

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

Source
  • homo sapiens (human)
  • severe acute respiratory syndrome coronavirus 2
KeywordsSTRUCTURAL PROTEIN / Trimer / Disulfide / Biologic scaffold / VIRAL PROTEIN/ANTAGONIST / trimeric antagonist SARS-CoV-2 complex / PROTEIN BINDING / VIRAL PROTEIN-ANTAGONIST 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