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Open data
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Basic information
Entry | Database: PDB / ID: 5h3o | ||||||||||||||||||||||||||||||||||||||||||||||||
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Title | Structure of a eukaryotic cyclic nucleotide-gated channel | ||||||||||||||||||||||||||||||||||||||||||||||||
![]() | Cyclic nucleotide-gated cation channel | ||||||||||||||||||||||||||||||||||||||||||||||||
![]() | TRANSPORT PROTEIN / TAX-4 / CNG / Channel / Open state | ||||||||||||||||||||||||||||||||||||||||||||||||
Function / homology | ![]() detection of carbon dioxide / detection of chemical stimulus involved in sensory perception / ciliary inversin compartment / Activation of the phototransduction cascade / Inactivation, recovery and regulation of the phototransduction cascade / VxPx cargo-targeting to cilium / thermosensory behavior / positive regulation of growth rate / olfactory behavior / aerotaxis ...detection of carbon dioxide / detection of chemical stimulus involved in sensory perception / ciliary inversin compartment / Activation of the phototransduction cascade / Inactivation, recovery and regulation of the phototransduction cascade / VxPx cargo-targeting to cilium / thermosensory behavior / positive regulation of growth rate / olfactory behavior / aerotaxis / chemosensory behavior / intracellular cyclic nucleotide activated cation channel complex / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / intracellularly cGMP-activated cation channel activity / cation channel complex / response to oxygen levels / intracellularly cAMP-activated cation channel activity / thermotaxis / multicellular organismal reproductive process / non-motile cilium / regulation of axon extension / regulation of neuron differentiation / negative regulation of cGMP-mediated signaling / voltage-gated potassium channel activity / monoatomic cation transmembrane transport / phototransduction / cGMP binding / response to hyperoxia / neuron projection morphogenesis / calcium-mediated signaling / chemotaxis / dendrite / protein-containing complex binding / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||
![]() | Li, M. / Zhou, X. / Wang, S. / Michailidis, I. / Gong, Y. / Su, D. / Li, H. / Li, X. / Yang, J. | ||||||||||||||||||||||||||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structure of a eukaryotic cyclic-nucleotide-gated channel. Authors: Minghui Li / Xiaoyuan Zhou / Shu Wang / Ioannis Michailidis / Ye Gong / Deyuan Su / Huan Li / Xueming Li / Jian Yang / ![]() ![]() Abstract: Cyclic-nucleotide-gated channels are essential for vision and olfaction. They belong to the voltage-gated ion channel superfamily but their activities are controlled by intracellular cyclic ...Cyclic-nucleotide-gated channels are essential for vision and olfaction. They belong to the voltage-gated ion channel superfamily but their activities are controlled by intracellular cyclic nucleotides instead of transmembrane voltage. Here we report a 3.5-Å-resolution single-particle electron cryo-microscopy structure of a cyclic-nucleotide-gated channel from Caenorhabditis elegans in the cyclic guanosine monophosphate (cGMP)-bound open state. The channel has an unusual voltage-sensor-like domain, accounting for its deficient voltage dependence. A carboxy-terminal linker connecting S6 and the cyclic-nucleotide-binding domain interacts directly with both the voltage-sensor-like domain and the pore domain, forming a gating ring that couples conformational changes triggered by cyclic nucleotide binding to the gate. The selectivity filter is lined by the carboxylate side chains of a functionally important glutamate and three rings of backbone carbonyls. This structure provides a new framework for understanding mechanisms of ion permeation, gating and channelopathy of cyclic-nucleotide-gated channels and cyclic nucleotide modulation of related channels. | ||||||||||||||||||||||||||||||||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 430.2 KB | Display | ![]() |
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PDB format | ![]() | 346.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 63.3 KB | Display | |
Data in CIF | ![]() | 94.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6656MC ![]() 6657C 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: 84305.898 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-PCG / #3: Chemical | |
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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: Cyclic nucleotide-gated (CNG) channels / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | |||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() | |||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was homogeneous | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.15 K Details: Blotted for 4.0 seconds (double-sided, blot force 1), after waiting for 3.0 seconds the grid was immediately plunged into liquid ethane cooled by liquid-nitrogen. |
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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 / Nominal magnification: 22500 X / Nominal defocus max: 2700 nm / Nominal defocus min: 1700 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 8 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Sampling size: 5 µm / Width: 7676 / Height: 7420 / Movie frames/image: 32 / Used frames/image: 1-32 |
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Processing
EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99934 / Symmetry type: POINT |