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Yorodumi- PDB-6vy0: SthK P300A cyclic nucleotide-gated potassium channel in a putativ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vy0 | ||||||||||||
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Title | SthK P300A cyclic nucleotide-gated potassium channel in a putative active state, in complex with cAMP | ||||||||||||
Components | SthK | ||||||||||||
Keywords | TRANSPORT PROTEIN | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Spirochaeta thermophila DSM 6578 (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.68 Å | ||||||||||||
Authors | Schmidpeter, P.A.M. / Rheinberger, J. / Nimigean, C.M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2020 Title: Prolyl isomerization controls activation kinetics of a cyclic nucleotide-gated ion channel. Authors: Philipp A M Schmidpeter / Jan Rheinberger / Crina M Nimigean / Abstract: SthK, a cyclic nucleotide-modulated ion channel from Spirochaeta thermophila, activates slowly upon cAMP increase. This is reminiscent of the slow, cAMP-induced activation reported for the ...SthK, a cyclic nucleotide-modulated ion channel from Spirochaeta thermophila, activates slowly upon cAMP increase. This is reminiscent of the slow, cAMP-induced activation reported for the hyperpolarization-activated and cyclic nucleotide-gated channel HCN2 in the family of so-called pacemaker channels. Here, we investigate slow cAMP-induced activation in purified SthK channels using stopped-flow assays, mutagenesis, enzymatic catalysis and inhibition assays revealing that the cis/trans conformation of a conserved proline in the cyclic nucleotide-binding domain determines the activation kinetics of SthK. We propose that SthK exists in two forms: trans Pro300 SthK with high ligand binding affinity and fast activation, and cis Pro300 SthK with low affinity and slow activation. Following channel activation, the cis/trans equilibrium, catalyzed by prolyl isomerases, is shifted towards trans, while steady-state channel activity is unaffected. Our results reveal prolyl isomerization as a regulatory mechanism for SthK, and potentially eukaryotic HCN channels. This mechanism could contribute to electrical rhythmicity in cells. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6vy0.cif.gz | 219.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vy0.ent.gz | 150.9 KB | Display | PDB format |
PDBx/mmJSON format | 6vy0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/6vy0 ftp://data.pdbj.org/pub/pdb/validation_reports/vy/6vy0 | HTTPS FTP |
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-Related structure data
Related structure data | 21454MC 6vxzC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 51092.539 Da / Num. of mol.: 4 / Mutation: P300A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Spirochaeta thermophila DSM 6578 (bacteria) Strain: ATCC 700085 / DSM 6578 / Z-1203 / Gene: Spith_0644 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: G0GA88 |
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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: SthK P300A bound to cAMP / Type: COMPLEX Details: Low-populated state of SthK P300A reconstituted into nanodiscs. Due to the low resolution, side chains could not be assigned and all amino acids are modeled as alanine. The register is ...Details: Low-populated state of SthK P300A reconstituted into nanodiscs. Due to the low resolution, side chains could not be assigned and all amino acids are modeled as alanine. The register is maintained from the high-resolution structure of the closed state. Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Spirochaeta thermophila (strain ATCC 700085 / DSM 6578 / Z-1203) (bacteria) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: C41(DE3) | |||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 7.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K |
-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 FIELDBright-field microscopy / Nominal magnification: 105000 X / Calibrated magnification: 45620 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm / Cs: 0.001 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 71 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2494 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV Spherical aberration corrector: Microscope was modified with a Cs corrector |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 50 / Used frames/image: 1-50 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 657943 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 6.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19918 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Space: REAL |