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Yorodumi- PDB-9b94: Cryo-EM structure of the E396A mutant of human TRPM4 in complex w... -
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-Basic information
Entry | Database: PDB / ID: 9b94 | ||||||||||||||||||||||||||||||
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Title | Cryo-EM structure of the E396A mutant of human TRPM4 in complex with calcium at 37 degrees Celsius | ||||||||||||||||||||||||||||||
Components | Transient receptor potential cation channel subfamily M member 4 | ||||||||||||||||||||||||||||||
Keywords | MEMBRANE PROTEIN / ion channel / TRP 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 / membrane depolarization during bundle of His cell action potential / membrane depolarization during Purkinje myocyte cell action potential / negative regulation of bone mineralization / ligand-gated calcium channel activity / sodium ion import across plasma membrane ...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 / membrane depolarization during bundle of His cell action potential / membrane depolarization during Purkinje myocyte cell action potential / negative regulation of bone mineralization / ligand-gated calcium channel activity / sodium ion import across plasma membrane / regulation of ventricular cardiac muscle cell action potential / calcium-activated cation channel activity / inorganic cation transmembrane transport / TRP channels / dendritic cell chemotaxis / sodium channel activity / cellular response to ATP / positive regulation of heart rate / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / regulation of heart rate by cardiac conduction / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of vasoconstriction / protein sumoylation / positive regulation of adipose tissue development / calcium ion transmembrane transport / calcium-mediated signaling / 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 / Golgi apparatus / endoplasmic reticulum / nucleoplasm / ATP binding / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||||||||||||||||||||
Authors | Hu, J. / Lu, W. / Du, J. | ||||||||||||||||||||||||||||||
Funding support | United States, 9items
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Citation | Journal: Nature / Year: 2024 Title: Physiological temperature drives TRPM4 ligand recognition and gating. Authors: Jinhong Hu / Sung Jin Park / Tyler Walter / Ian J Orozco / Garrett O'Dea / Xinyu Ye / Juan Du / Wei Lü / Abstract: Temperature profoundly affects macromolecular function, particularly in proteins with temperature sensitivity. However, its impact is often overlooked in biophysical studies that are typically ...Temperature profoundly affects macromolecular function, particularly in proteins with temperature sensitivity. However, its impact is often overlooked in biophysical studies that are typically performed at non-physiological temperatures, potentially leading to inaccurate mechanistic and pharmacological insights. Here we demonstrate temperature-dependent changes in the structure and function of TRPM4, a temperature-sensitive Ca-activated ion channel. By studying TRPM4 prepared at physiological temperature using single-particle cryo-electron microscopy, we identified a 'warm' conformation that is distinct from those observed at lower temperatures. This conformation is driven by a temperature-dependent Ca-binding site in the intracellular domain, and is essential for TRPM4 function in physiological contexts. We demonstrated that ligands, exemplified by decavanadate (a positive modulator) and ATP (an inhibitor), bind to different locations of TRPM4 at physiological temperatures than at lower temperatures, and that these sites have bona fide functional relevance. We elucidated the TRPM4 gating mechanism by capturing structural snapshots of its different functional states at physiological temperatures, revealing the channel opening that is not observed at lower temperatures. Our study provides an example of temperature-dependent ligand recognition and modulation of an ion channel, underscoring the importance of studying macromolecules at physiological temperatures. It also provides a potential molecular framework for deciphering how thermosensitive TRPM channels perceive temperature changes. | ||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 9b94.cif.gz | 743.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9b94.ent.gz | 593.9 KB | Display | PDB format |
PDBx/mmJSON format | 9b94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9b94_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 9b94_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 9b94_validation.xml.gz | 98.8 KB | Display | |
Data in CIF | 9b94_validation.cif.gz | 150.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/9b94 ftp://data.pdbj.org/pub/pdb/validation_reports/b9/9b94 | HTTPS FTP |
-Related structure data
Related structure data | 44368MC 9b8wC 9b8xC 9b8yC 9b8zC 9b90C 9b91C 9b92C 9b93C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 134398.453 Da / Num. of mol.: 4 / Mutation: E396A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRPM4, LTRPC4 / Production host: Mammalia (mammals) / References: UniProt: Q8TD43 #2: Chemical | ChemComp-CA / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cryo-EM structure of the E396A mutant of human TRPM4 in complex with calcium at 37 degrees Celsius Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Mammalia (mammals) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1900 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 478000 / Symmetry type: POINT | ||||||||||||||||||||||||
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