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- PDB-5wp6: Cryo-EM structure of a human TRPM4 channel in complex with calciu... -

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Basic information

Entry
Database: PDB / ID: 5wp6
TitleCryo-EM structure of a human TRPM4 channel in complex with calcium and decavanadate
ComponentsTransient receptor potential cation channel subfamily M member 4
KeywordsMEMBRANE PROTEIN / Ion channel
Function / homology
Function and homology information


positive regulation of atrial cardiac muscle cell action potential / positive regulation of regulation of vascular associated smooth muscle cell membrane depolarization / sodium channel complex / regulation of T cell cytokine production / membrane depolarization during AV node cell action potential / metal ion transport / membrane depolarization during bundle of His cell action potential / membrane depolarization during Purkinje myocyte cell action potential / negative regulation of bone mineralization / regulation of ventricular cardiac muscle cell action potential ...positive regulation of atrial cardiac muscle cell action potential / positive regulation of regulation of vascular associated smooth muscle cell membrane depolarization / sodium channel complex / regulation of T cell cytokine production / membrane depolarization during AV node cell action potential / metal ion transport / membrane depolarization during bundle of His cell action potential / membrane depolarization during Purkinje myocyte cell action potential / negative regulation of bone mineralization / regulation of ventricular cardiac muscle cell action potential / calcium-activated cation channel activity / sodium ion import across plasma membrane / inorganic cation transmembrane transport / dendritic cell chemotaxis / TRP channels / cellular response to ATP / sodium channel activity / monoatomic cation transmembrane transport / regulation of heart rate by cardiac conduction / positive regulation of insulin secretion involved in cellular response to glucose stimulus / protein sumoylation / negative regulation of osteoblast differentiation / positive regulation of fat cell differentiation / positive regulation of heart rate / positive regulation of adipose tissue development / positive regulation of vasoconstriction / calcium-mediated signaling / calcium ion transmembrane transport / calcium channel activity / Sensory perception of sweet, bitter, and umami (glutamate) taste / positive regulation of canonical Wnt signaling pathway / positive regulation of cytosolic calcium ion concentration / protein homotetramerization / adaptive immune response / calmodulin binding / neuronal cell body / positive regulation of cell population proliferation / calcium ion binding / endoplasmic reticulum / Golgi apparatus / nucleoplasm / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
TRPM, SLOG domain / : / SLOG in TRPM / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
DECAVANADATE / Transient receptor potential cation channel subfamily M member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWinkler, P.A. / Huang, Y. / Sun, W. / Du, J. / Lu, W.
CitationJournal: Nature / Year: 2017
Title: Electron cryo-microscopy structure of a human TRPM4 channel.
Authors: Paige A Winkler / Yihe Huang / Weinan Sun / Juan Du / Wei Lü /
Abstract: Ca-activated, non-selective (CAN) ion channels sense increases of the intracellular Ca concentration, producing a flux of Na and/or K ions that depolarizes the cell, thus modulating cellular Ca entry. ...Ca-activated, non-selective (CAN) ion channels sense increases of the intracellular Ca concentration, producing a flux of Na and/or K ions that depolarizes the cell, thus modulating cellular Ca entry. CAN channels are involved in cellular responses such as neuronal bursting activity and cardiac rhythm. Here we report the electron cryo-microscopy structure of the most widespread CAN channel, human TRPM4, bound to the agonist Ca and the modulator decavanadate. Four cytosolic C-terminal domains form an umbrella-like structure with a coiled-coil domain for the 'pole' and four helical 'ribs' spanning the N-terminal TRPM homology regions (MHRs), thus holding four subunits in a crown-like architecture. We observed two decavanadate-binding sites, one in the C-terminal domain and another in the intersubunit MHR interface. A glutamine in the selectivity filter may be an important determinant of monovalent selectivity. Our structure provides new insights into the function and pharmacology of both the CAN and the TRPM families.
History
DepositionAug 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
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Revision 1.0Dec 13, 2017Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 13, 2017Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
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Revision 1.3Mar 29, 2023Group: Database references / Category: database_2 / pdbx_database_related
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Revision 1.4May 15, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5May 28, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily M member 4
B: Transient receptor potential cation channel subfamily M member 4
C: Transient receptor potential cation channel subfamily M member 4
D: Transient receptor potential cation channel subfamily M member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)545,48512
Polymers537,8264
Non-polymers7,6598
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area31140 Å2
ΔGint-305 kcal/mol
Surface area199790 Å2

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Components

#1: Protein
Transient receptor potential cation channel subfamily M member 4 / hTRPM4 / Calcium-activated non-selective cation channel 1 / Long transient receptor potential ...hTRPM4 / Calcium-activated non-selective cation channel 1 / Long transient receptor potential channel 4 / LTrpC4 / Melastatin-4


Mass: 134456.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRPM4, LTRPC4 / Production host: Homo sapiens (human) / References: UniProt: Q8TD43
#2: Chemical
ChemComp-DVT / DECAVANADATE


Mass: 957.398 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: O28V10
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: TRPM4 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.54 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 54 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12rc1_2815: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121906 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00929488
ELECTRON MICROSCOPYf_angle_d0.97440204
ELECTRON MICROSCOPYf_dihedral_angle_d15.20717188
ELECTRON MICROSCOPYf_chiral_restr0.0544684
ELECTRON MICROSCOPYf_plane_restr0.0085088

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