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Yorodumi- PDB-5vkq: Structure of a mechanotransduction ion channel Drosophila NOMPC i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vkq | ||||||||||||||||||||||||
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Title | Structure of a mechanotransduction ion channel Drosophila NOMPC in nanodisc | ||||||||||||||||||||||||
Components | No mechanoreceptor potential C isoform L | ||||||||||||||||||||||||
Keywords | MEMBRANE PROTEIN / Mechanotransduction Ion channel | ||||||||||||||||||||||||
Function / homology | Function and homology information : / sensory perception of touch / detection of mechanical stimulus involved in sensory perception of touch / detection of mechanical stimulus involved in sensory perception / mechanosensory behavior / response to auditory stimulus / sensory perception of mechanical stimulus / cation channel complex / mechanosensitive monoatomic ion channel activity / locomotion ...: / sensory perception of touch / detection of mechanical stimulus involved in sensory perception of touch / detection of mechanical stimulus involved in sensory perception / mechanosensory behavior / response to auditory stimulus / sensory perception of mechanical stimulus / cation channel complex / mechanosensitive monoatomic ion channel activity / locomotion / ankyrin binding / startle response / monoatomic cation transport / monoatomic cation channel activity / sensory perception of sound / calcium channel activity / cilium / cellular response to mechanical stimulus / calcium ion transport / monoatomic ion channel activity / neuronal cell body / dendrite Similarity search - Function | ||||||||||||||||||||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.55 Å | ||||||||||||||||||||||||
Authors | Jin, P. / Bulkley, D. / Guo, Y. / Zhang, W. / Guo, Z. / Huynh, W. / Wu, S. / Meltzer, S. / Chen, T. / Jan, L.Y. ...Jin, P. / Bulkley, D. / Guo, Y. / Zhang, W. / Guo, Z. / Huynh, W. / Wu, S. / Meltzer, S. / Chen, T. / Jan, L.Y. / Jan, Y.-N. / Cheng, Y. | ||||||||||||||||||||||||
Funding support | United States, 7items
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Citation | Journal: Nature / Year: 2017 Title: Electron cryo-microscopy structure of the mechanotransduction channel NOMPC. Authors: Peng Jin / David Bulkley / Yanmeng Guo / Wei Zhang / Zhenhao Guo / Walter Huynh / Shenping Wu / Shan Meltzer / Tong Cheng / Lily Yeh Jan / Yuh-Nung Jan / Yifan Cheng / Abstract: Mechanosensory transduction for senses such as proprioception, touch, balance, acceleration, hearing and pain relies on mechanotransduction channels, which convert mechanical stimuli into electrical ...Mechanosensory transduction for senses such as proprioception, touch, balance, acceleration, hearing and pain relies on mechanotransduction channels, which convert mechanical stimuli into electrical signals in specialized sensory cells. How force gates mechanotransduction channels is a central question in the field, for which there are two major models. One is the membrane-tension model: force applied to the membrane generates a change in membrane tension that is sufficient to gate the channel, as in the bacterial MscL channel and certain eukaryotic potassium channels. The other is the tether model: force is transmitted via a tether to gate the channel. The transient receptor potential (TRP) channel NOMPC is important for mechanosensation-related behaviours such as locomotion, touch and sound sensation across different species including Caenorhabditis elegans, Drosophila and zebrafish. NOMPC is the founding member of the TRPN subfamily, and is thought to be gated by tethering of its ankyrin repeat domain to microtubules of the cytoskeleton. Thus, a goal of studying NOMPC is to reveal the underlying mechanism of force-induced gating, which could serve as a paradigm of the tether model. NOMPC fulfils all the criteria that apply to mechanotransduction channels and has 29 ankyrin repeats, the largest number among TRP channels. A key question is how the long ankyrin repeat domain is organized as a tether that can trigger channel gating. Here we present a de novo atomic structure of Drosophila NOMPC determined by single-particle electron cryo-microscopy. Structural analysis suggests that the ankyrin repeat domain of NOMPC resembles a helical spring, suggesting its role of linking mechanical displacement of the cytoskeleton to the opening of the channel. The NOMPC architecture underscores the basis of translating mechanical force into an electrical signal within a cell. | ||||||||||||||||||||||||
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 | 5vkq.cif.gz | 972.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vkq.ent.gz | 769.8 KB | Display | PDB format |
PDBx/mmJSON format | 5vkq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vkq_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 5vkq_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 5vkq_validation.xml.gz | 169.4 KB | Display | |
Data in CIF | 5vkq_validation.cif.gz | 248.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/5vkq ftp://data.pdbj.org/pub/pdb/validation_reports/vk/5vkq | HTTPS FTP |
-Related structure data
Related structure data | 8702MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10093 (Title: Structure of an ion channel in nano disc / Data size: 203.9 Data #1: Motion corrected dose weighted summed frames [micrographs - single frame] Data #2: Motion corrected dose weighted particle images [picked particles - multiframe - processed]) |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 188978.734 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: nompC, CG11020, Dmel_CG11020 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: E0A9E1 #2: Chemical | ChemComp-PCF / |
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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: Tetrameric channel / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.754893 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Drosophila melanogaster (fruit fly) | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 | ||||||||||||||||||||
Buffer solution | pH: 8.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 3.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: sample solubilized in nanodisc | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 92 % / Chamber temperature: 20 K Details: 2.5 sec blot, -1 offset, whatman #1 filter paper on front side, plastic on back side |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 31000 X / Calibrated magnification: 41132 X / Nominal defocus max: -3000 nm / Nominal defocus min: -1500 nm / Calibrated defocus min: -1400 nm / Calibrated defocus max: -3300 nm / Cs: 2.1 mm / C2 aperture diameter: 30 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN HCHST 3008 SINGLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER Temperature (max): 83 K / Temperature (min): 83 K |
Image recording | Average exposure time: 8 sec. / Electron dose: 54 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1873 |
Image scans | Sampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 2-40 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 190879 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 175314 / Num. of class averages: 5 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 125.7 / Protocol: AB INITIO MODEL / Space: REAL |