[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

TitleAllosteric activators of cystathionine γ lyase to augment endogenous hydrogen sulfide and inhibit pathologic calcification.
Journal, issue, pagesPharmacol Res, Vol. 219, Page 107869, Year 2025
Publish dateJul 26, 2025
AuthorsSonia Nasi / Driss Ehirchiou / Cindy Blatter / Veronique Chobaz / Stefan Germann / Alexandra Brandenberger / Elias Bommeli / Emiko Uchikawa / Giuseppe Cirino / Rainer Riedl / Alexander So / Nathalie Busso /
PubMed AbstractHydrogen sulfide (H₂S), a gasotransmitter naturally produced in the body by enzymes such as cystathionine γ lyase (CSE), helps reduce inflammation, oxidative stress, and abnormal tissue ...Hydrogen sulfide (H₂S), a gasotransmitter naturally produced in the body by enzymes such as cystathionine γ lyase (CSE), helps reduce inflammation, oxidative stress, and abnormal tissue calcification. We present a novel strategy to boost endogenous H₂S production via CSE allosteric activation. Two CSE positive allosteric modulators (CSE-PAMs) were identified. Despite moderate binding affinity, both compounds induced a strong allosteric effect, increasing H₂S production by approximately 200 %. Cryo-electron microscopy and proteomics identified a distinct allosteric binding pocket on recombinant human CSE. In cellular assays, both compounds elevated H₂S levels. This correlated with inhibition of calcification. In chondrocytes, CSE-PAMs reduced alkaline phosphatase activity, inflammatory cytokine secretion, and oxidative stress, while enhancing protein persulfidation. These results highlight CSE-PAMs as promising therapeutic agents for conditions involving pathological calcification and inflammation, such as osteoarthritis. Additionally, they serve as valuable tools for investigating CSE-derived H₂S biology, previously limited by a lack of specific modulators.
External linksPharmacol Res / PubMed:40716475
MethodsEM (single particle)
Resolution2.06 - 2.52 Å
Structure data

EMDB-52956: Structure of Cystathionine gamma-lyase with ZHAWOC24000
Method: EM (single particle) / Resolution: 2.52 Å

EMDB-52957: Structure of Cystathionine gamma-lyase
Method: EM (single particle) / Resolution: 2.06 Å

Source
  • Homo sapiens (human)

+
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