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- EMDB-70771: Cryo-EM structure of rat TRPM1 in the apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-70771
TitleCryo-EM structure of rat TRPM1 in the apo state
Map datasharpened main map focusing on the entire protein, refined in C1, Bfactor 31.5
Sample
  • Complex: apo tetrameric TRPM1
    • Protein or peptide: Isoform 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsFabrizio M / Zhao C
Funding support United States, 3 items
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, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70771.png

Downloads & links

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Map

FileDownload / File: emd_70771.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened main map focusing on the entire protein, refined in C1, Bfactor 31.5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 416 pix.
= 396.864 Å		0.95 Å/pix.
x 416 pix.
= 396.864 Å		0.95 Å/pix.
x 416 pix.
= 396.864 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.954 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0779
Minimum - Maximum-0.14365621 - 0.33146086
Average (Standard dev.)0.00018328562 (±0.01315313)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 396.864 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened main map focusing on the entire protein,...

Fileemd_70771_additional_1.map
Annotationunsharpened main map focusing on the entire protein, refined in C1, Bfactor 31.5
Projections & Slices
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Additional map: unsharpened map focusing on the entire protein, refined...

Fileemd_70771_additional_2.map
Annotationunsharpened map focusing on the entire protein, refined in C2, Bfactor 53.2
Projections & Slices
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Additional map: unsharpened map focusing on the intracellular domain, refined...

Fileemd_70771_additional_3.map
Annotationunsharpened map focusing on the intracellular domain, refined in C1, Bfactor 93.8
Projections & Slices
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Additional map: sharpened map focusing on the intracellular domain, refined...

Fileemd_70771_additional_4.map
Annotationsharpened map focusing on the intracellular domain, refined in C1, Bfactor 93.8
Projections & Slices
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Additional map: #1

Fileemd_70771_additional_5.map
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Half map: half map 2 for the main map

Fileemd_70771_half_map_1.map
Annotationhalf map 2 for the main map
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Half map: half map 1 for the main map

Fileemd_70771_half_map_2.map
Annotationhalf map 1 for the main map
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Sample components

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Entire : apo tetrameric TRPM1

EntireName: apo tetrameric TRPM1
Components
  • Complex: apo tetrameric TRPM1
    • Protein or peptide: Isoform 2 of Transient receptor potential cation channel subfamily M member 1

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Supramolecule #1: apo tetrameric TRPM1

SupramoleculeName: apo tetrameric TRPM1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Isoform 2 of Transient receptor potential cation channel subfamil...

MacromoleculeName: Isoform 2 of Transient receptor potential cation channel subfamily M member 1
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 156.695719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSMRKMSSS FKRGSIKSST SGSQKGQKAW IEKTFCKREC IFVIPSTKDP NRCCCGQLTN QHIPPLPSVT PSSTAEDTKQ GDAQSGKWS VSKHTQSYPT DSYGILEFQG GGYSNKAMYI RVSYDTKPDS LLHLMVKDWQ LELPKLLISV HGGLQSFEMQ P KLKQVFGK ...String:
MGSMRKMSSS FKRGSIKSST SGSQKGQKAW IEKTFCKREC IFVIPSTKDP NRCCCGQLTN QHIPPLPSVT PSSTAEDTKQ GDAQSGKWS VSKHTQSYPT DSYGILEFQG GGYSNKAMYI RVSYDTKPDS LLHLMVKDWQ LELPKLLISV HGGLQSFEMQ P KLKQVFGK GLIKAAMTTG AWIFTGGVST GVVSHVGDAL KDHSSKSRGR LCAIGIAPWG MVENKEDLVG KDVTRVYQTM SN PLSKLSV LNNSHTHFIL ADNGTLGKYG AEVKLRRQLE KHISLQKINT RLGQGVPVVG LVVEGGPNVV SIVLEYLRED PPV PVVVCD GSGRASDILS FAHKYCDEGG VINESLRDQL LVTIQKTFNY SKSQSHQLFA IIMECMKKKE LVTVFRMGSE GQQD VEMAI LTALLKGTNV SAPDQLSLAL AWNRVDIARS QIFVFGPHWP PLGSLAPPVD TKVAEKEKKP PTATTKGRGK GKGKK KGKV KEEVEEETDP RKIELLNWVN ALEQAMLDAL VLDRVDFVKL LIENGVNMQH FLTIPRLEEL YNTRLGPPNT LHLLVR DVK KSNLPPDYHI SLIDIGLVLE YLMGGAYRCN YTRKSFRTLY NNLFGPKRPK ALKLLGMEDD EPPAKGKKKK KKKKEEE ID IDVDDPAVSR FQYPFHELMV WAVLMKRQKM AVFLWQRGEE CMAKALVACK LYKAMAHESS ESELVDDISQ DLDNNSKD F GQLAVELLDQ SYKHDEQVAM KLLTYELKNW SNSTCLKLAV AAKHRDFIAH TCSQMLLTDM WMGRLRMRKN PGLKVIMGI LIPPTILFLE FRSYDDFSYQ TSKENEDGKE KEEENVDANA DAGSRKGDEE NEHKKQRSIP IGTKICEFYN APIVKFWFYT ISYLGYLLL FNYVILVRMD GWPSPQEWIV ISYIVSLALE KIREILMSEP GKLSQKIKVW LQEYWNITDL VAISMFMVGA I LRLQNQPY MGYGRVIYCV DIILWYIRVL DIFGVNKYLG PYVMMIGKMM IDMLYFVVIM LVVLMSFGVA RQAILHPEEK PS WKLARNI FYMPYWMIYG EVFADQIDLY AMEINPPCGE NLYDEEGKRL PPCIPGAWLT PALMACYLLV ANILLVNLLI AVF NNTFFE VKSISNQVWK FQRYQLIMTF HDRPVLPPPM IILSHIYIIV MRLSGRCRKK REGDQEERDR GLKLFLSDEE LKKL HEFEE QCVQEHFREK EDEQQSSSDE RIRVTSERVE NMSMRLEEIN ERENFMKASL QTVDLRLSQL EELSGRMVGA LENLA GIDR SDLIQARSRA SSECEATYLL RQSSINSADG YSMYRYHFNG EELLFEEPAL STSPGTVFRK KTCSFRVPSR LEEELR RRL TENSLEVLFQ

UniProtKB: Transient receptor potential cation channel subfamily M member 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab-initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 18202
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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