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- PDB-9or5: Cryo-EM structure of rat TRPM1 in the apo state -

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Basic information

Entry
Database: PDB / ID: 9or5
TitleCryo-EM structure of rat TRPM1 in the apo state
ComponentsIsoform 2 of Transient receptor potential cation channel subfamily M member 1
KeywordsMEMBRANE PROTEIN / TRPM1 / ion channel
Function / homology
Function and homology information


new growing cell tip / retinal rod cell development / cellular response to light stimulus / cell tip / TRP channels / G protein-coupled glutamate receptor signaling pathway / monoatomic cation transmembrane transporter activity / calcium ion import across plasma membrane / monoatomic cation transmembrane transport / monoatomic ion channel activity ...new growing cell tip / retinal rod cell development / cellular response to light stimulus / cell tip / TRP channels / G protein-coupled glutamate receptor signaling pathway / monoatomic cation transmembrane transporter activity / calcium ion import across plasma membrane / monoatomic cation transmembrane transport / monoatomic ion channel activity / monoatomic cation channel activity / visual perception / protein tetramerization / calcium channel activity / calcium ion transport / intracellular protein localization / axon / dendrite / endoplasmic reticulum membrane / endoplasmic reticulum / signal transduction / plasma membrane
Similarity search - Function
TRPM, tetramerisation domain / TRPM, tetramerisation domain superfamily / Tetramerisation domain of TRPM / TRPM, SLOG domain / : / : / SLOG in TRPM / TRPM2-like domain / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily M member 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsFabrizio, M. / Zhao, C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R24GM154186 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R24GM145964 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R24GM154185 United States
CitationJournal: Nat Commun / Year: 2026
Title: Cryo-EM structure of TRPM1 reveals a non-canonical architecture with an inverted transmembrane domain.
Authors: Michael Fabrizio / Mackenzie Brewer / Nebojša Bogdanović / Chen Zhao /
Abstract: Transient receptor potential melastatin 1 (TRPM1) is a membrane protein essential for vision in dim light, and mutations in TRPM1 cause complete congenital stationary night blindness. Although TRPM1 ...Transient receptor potential melastatin 1 (TRPM1) is a membrane protein essential for vision in dim light, and mutations in TRPM1 cause complete congenital stationary night blindness. Although TRPM1 shares sequence similarity to other TRPM ion channels such as TRPM3, whether it independently functions as an ion channel remains controversial. This controversy is largely caused by TRPM1's challenging biochemical behaviors that prevent detailed molecular characterization. In this work, we isolate TRPM1 and determine its structures using cryogenic electron microscopy (cryo-EM). The structures reveal a canonical tetrameric fold in the intracellular domain, consistent with other TRPM family members that are ion channels. Surprisingly, in the transmembrane domain, despite the presence of the conserved voltage sensor-like domain (VSLD) and pore domain (PD) in a domain-swapped fashion, the VSLD and PD are arranged with an opposite handedness compared to other related channels. This inverted transmembrane domain allows the formation of a large pore-like structure that supports the role of TRPM1 as an ion channel. This non-canonical architecture of TRPM1 may also confer unique permeation and pharmacological properties.
History
DepositionMay 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Additional map / Part number: 4 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Additional map / Part number: 5 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of Transient receptor potential cation channel subfamily M member 1
B: Isoform 2 of Transient receptor potential cation channel subfamily M member 1
C: Isoform 2 of Transient receptor potential cation channel subfamily M member 1
D: Isoform 2 of Transient receptor potential cation channel subfamily M member 1


Theoretical massNumber of molelcules
Total (without water)626,7834
Polymers626,7834
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Isoform 2 of Transient receptor potential cation channel subfamily M member 1 / Melastatin-1


Mass: 156695.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Trpm1 / Production host: Homo sapiens (human) / References: UniProt: Q2WEA5
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: apo tetrameric TRPM1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13PHENIX3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18202 / Symmetry type: POINT

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