[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

TitleMembrane-forming phospholipids allosterically modulate native-state prolyl isomerization in a CNG channel.
Journal, issue, pagesProtein Sci, Vol. 34, Issue 12, Page e70383, Year 2025
Publish dateNov 20, 2025
AuthorsAshley J Newton / Robert D Latvala / Adefoluke E Kuforiji / Philipp A M Schmidpeter /
PubMed AbstractIon channel activity is intricately linked to the surrounding lipid environment, yet the molecular effects of lipid-mediated regulation remain largely understudied. Here, we show that membrane- ...Ion channel activity is intricately linked to the surrounding lipid environment, yet the molecular effects of lipid-mediated regulation remain largely understudied. Here, we show that membrane-forming phospholipids, which are known to modulate the activity of the cyclic nucleotide-gated channel SthK from Spirochaeta thermophila, exhibit effects that extend well beyond the membrane boundary. Using stopped-flow flux assays, we demonstrate that anionic lipids, which are known to promote channel opening, also affect the fast-to-slow activation ratio and the cAMP potency in SthK. Enzymatic catalysis studies confirm that this occurs by altering the cis/trans equilibrium at Pro300 in the apo state. Additionally, cryogenic electron microscopy structures of SthK reveal lipid-dependent conformational changes that propagate from the bundle crossing into the cytosolic domains. All observed effects correlate with the electronegativity of the lipid headgroup, indicating a common underlying mechanism. Our results highlight membrane-forming phospholipids as allosteric regulators of SthK, controlling multiple functional characteristics of the channel.
External linksProtein Sci / PubMed:41263484 / PubMed Central
MethodsEM (single particle)
Resolution2.69 - 2.74 Å
Structure data

49883

9nwj

EMDB-49883, PDB-9nwj:
Apo WT SthK in 3:1 DOPC:POPE nanodiscs
Method: EM (single particle) / Resolution: 2.69 Å

49884

9nwk

EMDB-49884, PDB-9nwk:
cAMP-bound WT SthK in 3:1 DOPC:POPE nanodiscs
Method: EM (single particle) / Resolution: 2.74 Å

Chemicals

ChemComp-6OU:
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate / phospholipid*YM

ChemComp-CMP:
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

Source
  • spirochaeta thermophila (bacteria)
KeywordsMEMBRANE PROTEIN / trans-membrane protein ion channel cyclic nucleotide-gated channel

+
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