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Open data
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Basic information
Entry | Database: PDB / ID: 6cx0 | ||||||
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Title | Structure of AtTPC1 D376A | ||||||
![]() | Two pore calcium channel protein 1 | ||||||
![]() | membrane protein/inhibitor / Ion channel / Two-pore channel / TPC1 / resting-state / closed / inactive / MEMBRANE PROTEIN / membrane protein-inhibitor complex | ||||||
Function / homology | ![]() regulation of jasmonic acid biosynthetic process / seed germination / regulation of stomatal movement / plant-type vacuole / vacuole / vacuolar membrane / monoatomic ion channel complex / voltage-gated calcium channel activity / calcium-mediated signaling / calcium ion transport ...regulation of jasmonic acid biosynthetic process / seed germination / regulation of stomatal movement / plant-type vacuole / vacuole / vacuolar membrane / monoatomic ion channel complex / voltage-gated calcium channel activity / calcium-mediated signaling / calcium ion transport / calcium ion binding / Golgi apparatus / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kintzer, A.F. / Stroud, R.M. | ||||||
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![]() | ![]() Title: Structural basis for activation of voltage sensor domains in an ion channel TPC1. Authors: Alexander F Kintzer / Evan M Green / Pawel K Dominik / Michael Bridges / Jean-Paul Armache / Dawid Deneka / Sangwoo S Kim / Wayne Hubbell / Anthony A Kossiakoff / Yifan Cheng / Robert M Stroud / ![]() Abstract: Voltage-sensing domains (VSDs) couple changes in transmembrane electrical potential to conformational changes that regulate ion conductance through a central channel. Positively charged amino acids ...Voltage-sensing domains (VSDs) couple changes in transmembrane electrical potential to conformational changes that regulate ion conductance through a central channel. Positively charged amino acids inside each sensor cooperatively respond to changes in voltage. Our previous structure of a TPC1 channel captured an example of a resting-state VSD in an intact ion channel. To generate an activated-state VSD in the same channel we removed the luminal inhibitory Ca-binding site (Ca), which shifts voltage-dependent opening to more negative voltage and activation at 0 mV. Cryo-EM reveals two coexisting structures of the VSD, an intermediate state 1 that partially closes access to the cytoplasmic side but remains occluded on the luminal side and an intermediate activated state 2 in which the cytoplasmic solvent access to the gating charges closes, while luminal access partially opens. Activation can be thought of as moving a hydrophobic insulating region of the VSD from the external side to an alternate grouping on the internal side. This effectively moves the gating charges from the inside potential to that of the outside. Activation also requires binding of Ca to a cytoplasmic site (Ca). An X-ray structure with Ca removed and a near-atomic resolution cryo-EM structure with Ca removed define how dramatic conformational changes in the cytoplasmic domains may communicate with the VSD during activation. Together four structures provide a basis for understanding the voltage-dependent transition from resting to activated state, the tuning of VSD by thermodynamic stability, and this channel's requirement of cytoplasmic Ca ions for activation. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 143.8 KB | Display | ![]() |
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PDB format | ![]() | 109 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8956C ![]() 8957C ![]() 8958C ![]() 8960C ![]() 6e1kC ![]() 6e1mC ![]() 6e1nC ![]() 6e1pC ![]() 5dqqS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 84310.234 Da / Num. of mol.: 1 / Mutation: D376A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-FJ7 / ( | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.42 Å3/Da / Density % sol: 72.2 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 9.3 Details: Sitting drop 2microliter drops crystchem 0.1 M glycine, pH 9.3, 50 mM potassium chloride, 1 mM calcium chloride, 35% PEG300 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→30 Å / Num. obs: 19231 / % possible obs: 99.7 % / Redundancy: 13.6 % / Rrim(I) all: 0.239 / Net I/σ(I): 8.08 |
Reflection shell | Resolution: 3.5→4 Å / Num. unique obs: 6273 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DQQ Resolution: 3.501→41 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 51.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.501→41 Å
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Refine LS restraints |
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LS refinement shell |
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