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Open data
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Basic information
Entry | Database: PDB / ID: 6whg | |||||||||
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Title | PI3P and calcium bound full-length TRPY1 in detergent | |||||||||
![]() | Calcium channel YVC1 | |||||||||
![]() | MEMBRANE PROTEIN / Ion channel | |||||||||
Function / homology | ![]() TRP channels / vacuole-mitochondrion membrane contact site / intracellular monoatomic cation homeostasis / voltage-gated monoatomic ion channel activity / calcium-activated cation channel activity / fungal-type vacuole / sodium channel activity / calcium ion transmembrane import into cytosol / fungal-type vacuole membrane / plasma membrane => GO:0005886 ...TRP channels / vacuole-mitochondrion membrane contact site / intracellular monoatomic cation homeostasis / voltage-gated monoatomic ion channel activity / calcium-activated cation channel activity / fungal-type vacuole / sodium channel activity / calcium ion transmembrane import into cytosol / fungal-type vacuole membrane / plasma membrane => GO:0005886 / calcium ion import across plasma membrane / potassium channel activity / calcium channel activity / monoatomic ion channel activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Ahmed, T. / Moiseenkova-Bell, V.Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the ancient TRPY1 channel from Saccharomyces cerevisiae reveals mechanisms of modulation by lipids and calcium. Authors: Tofayel Ahmed / Collin R Nisler / Edwin C Fluck / Sanket Walujkar / Marcos Sotomayor / Vera Y Moiseenkova-Bell / ![]() Abstract: Transient receptor potential (TRP) channels emerged in fungi as mechanosensitive osmoregulators. The Saccharomyces cerevisiae vacuolar TRP yeast 1 (TRPY1) is the most studied TRP channel from fungi, ...Transient receptor potential (TRP) channels emerged in fungi as mechanosensitive osmoregulators. The Saccharomyces cerevisiae vacuolar TRP yeast 1 (TRPY1) is the most studied TRP channel from fungi, but the structure and details of channel modulation remain elusive. Here, we describe the full-length cryoelectron microscopy structure of TRPY1 at 3.1 Å resolution in a closed state. The structure, despite containing an evolutionarily conserved and archetypical transmembrane domain, reveals distinctive structural folds for the cytosolic N and C termini, compared with other eukaryotic TRP channels. We identify an inhibitory phosphatidylinositol 3-phosphate (PI(3)P) lipid-binding site, along with two Ca-binding sites: a cytosolic site, implicated in channel activation and a vacuolar lumen site, implicated in inhibition. These findings, together with data from microsecond-long molecular dynamics simulations and a model of a TRPY1 open state, provide insights into the basis of TRPY1 channel modulation by lipids and Ca, and the molecular evolution of TRP channels. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 387.8 KB | Display | ![]() |
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PDB format | ![]() | 309 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 21672MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 78034.602 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: YVC1, YOR087W, YOR088W, YOR3151W / Production host: ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-PWE / ( 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 |
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Sample preparation
Component | Name: PI3P and calcium bound full-length TRPY1 in detergent / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55593 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.44 Å2 | ||||||||||||||||||||||||
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