[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

TitleStructural dynamics at cytosolic interprotomer interfaces control gating of a mammalian TRPM5 channel.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 121, Issue 27, Page e2403333121, Year 2024
Publish dateJul 2, 2024
AuthorsSebastian Karuppan / Lynn Goss Schrag / Caroline M Pastrano / Andrés Jara-Oseguera / Lejla Zubcevic /
PubMed AbstractThe transient receptor potential melastatin (TRPM) tetrameric cation channels are involved in a wide range of biological functions, from temperature sensing and taste transduction to regulation of ...The transient receptor potential melastatin (TRPM) tetrameric cation channels are involved in a wide range of biological functions, from temperature sensing and taste transduction to regulation of cardiac function, inflammatory pain, and insulin secretion. The structurally conserved TRPM cytoplasmic domains make up >70 % of the total protein. To investigate the mechanism by which the TRPM cytoplasmic domains contribute to gating, we employed electrophysiology and cryo-EM to study TRPM5-a channel that primarily relies on activation via intracellular Ca. Here, we show that activation of mammalian TRPM5 channels is strongly altered by Ca-dependent desensitization. Structures of rat TRPM5 identify a series of conformational transitions triggered by Ca binding, whereby formation and dissolution of cytoplasmic interprotomer interfaces appear to control activation and desensitization of the channel. This study shows the importance of the cytoplasmic assembly in TRPM5 channel function and sets the stage for future investigations of other members of the TRPM family.
External linksProc Natl Acad Sci U S A / PubMed:38923985 / PubMed Central
MethodsEM (single particle)
Resolution3.5 - 5.0 Å
Structure data

40574

8sl6

EMDB-40574, PDB-8sl6:
Cryo-EM structure of the rat TRPM5 channel in EGTA
Method: EM (single particle) / Resolution: 4.3 Å

40575

8sl8

EMDB-40575, PDB-8sl8:
Cryo-EM structure of the rat TRPM5 channel in trace calcium, trace-1
Method: EM (single particle) / Resolution: 4.2 Å

40576

8sla

EMDB-40576, PDB-8sla:
Cryo-EM structure of the rat TRPM5 channel in trace calcium, trace-2
Method: EM (single particle) / Resolution: 3.7 Å

40577

8sle

EMDB-40577, PDB-8sle:
Cryo-EM structure of the rat TRPM5 channel in trace calcium, trace-3
Method: EM (single particle) / Resolution: 4.3 Å

40578

8sli

EMDB-40578, PDB-8sli:
Cryo-EM structure of the rat TRPM5 channel in 2mM calcium, high-1
Method: EM (single particle) / Resolution: 4.9 Å

40579

8slp

EMDB-40579, PDB-8slp:
Cryo-EM structure of the rat TRPM5 channel in 2mM calcium, high-2
Method: EM (single particle) / Resolution: 3.8 Å

40580

8slq

EMDB-40580, PDB-8slq:
Cryo-EM structure of the rat TRPM5 channel in 2mM calcium, high-3
Method: EM (single particle) / Resolution: 4.5 Å

40581

8slw

EMDB-40581, PDB-8slw:
Cryo-EM structure of the rat TRPM5 channel in 2mM calcium, high-4
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-40592: Focused map of the cytoplasmic domains of rat TRPM5, conformation high-4
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-40593: Focused map of the cytoplasmic domains of rat TRPM5, conformation high-3
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-40595: Focused map of the cytoplasmic domains of rat TRPM5, conformation high-2
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-40596: Focused map of the cytoplasmic domains of rat TRPM5, conformation high-1
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-40597: Focused map of the cytoplasmic domains of rat TRPM5, conformation trace-3
Method: EM (single particle) / Resolution: 5.0 Å

EMDB-40599: Focused map of the cytoplasmic domains of rat TRPM5, conformation trace-2
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-40600: Focused map of the cytoplasmic domains of rat TRPM5, conformation trace-1
Method: EM (single particle) / Resolution: 4.4 Å

Chemicals

ChemComp-CA:
Unknown entry

Source
  • rattus norvegicus (Norway rat)
KeywordsMEMBRANE PROTEIN / ion channel / Transient Receptor Potential / TRP / Transient Receptor Potential Melastatin 5 / TRPM5 / TRANSPORT PROTEIN

+
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