|Entry||Database: PDB / ID: 6cjt|
|Title||Structure of the SthK cyclic nucleotide-gated potassium channel in complex with cGMP|
|Components||SthK cyclic nucleotide-gated potassium channel|
|Keywords||TRANSPORT PROTEIN / ion channel / tetramer / lipid / cGMP|
|Function / homology||Cyclic nucleotide-binding domain / Potassium channel domain / RmlC-like jelly roll fold / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-binding-like / Cyclic nucleotide-binding domain / Ion channel / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding domain signature 2. / cAMP/cGMP binding motif profile. ...Cyclic nucleotide-binding domain / Potassium channel domain / RmlC-like jelly roll fold / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-binding-like / Cyclic nucleotide-binding domain / Ion channel / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding domain signature 2. / cAMP/cGMP binding motif profile. / integral component of membrane / Putative transcriptional regulator, Crp/Fnr family|
Function and homology information
|Specimen source||Spirochaeta thermophila (bacteria)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.46 Å resolution|
|Authors||Nimigean, C.M. / Rheinberger, J.|
|Citation||Journal: Elife / Year: 2018|
Title: Ligand discrimination and gating in cyclic nucleotide-gated ion channels from apo and partial agonist-bound cryo-EM structures.
Authors: Jan Rheinberger / Xiaolong Gao / Philipp Am Schmidpeter / Crina M Nimigean
Abstract: Cyclic nucleotide-modulated channels have important roles in visual signal transduction and pacemaking. Binding of cyclic nucleotides (cAMP/cGMP) elicits diverse functional responses in different ...Cyclic nucleotide-modulated channels have important roles in visual signal transduction and pacemaking. Binding of cyclic nucleotides (cAMP/cGMP) elicits diverse functional responses in different channels within the family despite their high sequence and structure homology. The molecular mechanisms responsible for ligand discrimination and gating are unknown due to lack of correspondence between structural information and functional states. Using single particle cryo-electron microscopy and single-channel recording, we assigned functional states to high-resolution structures of SthK, a prokaryotic cyclic nucleotide-gated channel. The structures for apo, cAMP-bound, and cGMP-bound SthK in lipid nanodiscs, correspond to no, moderate, and low single-channel activity, respectively, consistent with the observation that all structures are in resting, closed states. The similarity between apo and ligand-bound structures indicates that ligand-binding domains are strongly coupled to pore and SthK gates in an allosteric, concerted fashion. The different orientations of cAMP and cGMP in the 'resting' and 'activated' structures suggest a mechanism for ligand discrimination.
SummaryFull reportAbout validation report
|Date||Deposition: Feb 26, 2018 / Release: Aug 1, 2018|
|Structure viewer||Molecule: |
Downloads & links
A: SthK cyclic nucleotide-gated potassium channel
B: SthK cyclic nucleotide-gated potassium channel
C: SthK cyclic nucleotide-gated potassium channel
D: SthK cyclic nucleotide-gated potassium channel
Mass: 51118.574 Da / Num. of mol.: 4 / Source: (gene. exp.) Spirochaeta thermophila (bacteria) / Strain: ATCC 700085 / DSM 6578 / Z-1203 / Gene: Spith_0644 / Production host: Escherichia coli (E. coli) / References: UniProt: G0GA88
ChemComp-PGW / (
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: single particle reconstruction|
|Component||Name: SthK cyclic nucleotide-gated potassium channel / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT|
|Molecular weight||Experimental value: NO|
|Source (natural)||Organism: Spirochaeta thermophila DSM 6578 (bacteria)|
|Source (recombinant)||Organism: Escherichia coli (E. coli)|
|Buffer solution||pH: 8|
|Specimen||Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope 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|
|Image recording||Electron dose: 52 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Symmetry||Point symmetry: C4|
|3D reconstruction||Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 91800 / Symmetry type: POINT|
|Least-squares process||Highest resolution: 3.46 Å|
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