+Open data
-Basic information
Entry | Database: PDB / ID: 8tdk | ||||||
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Title | Cryo-EM structure of AtMSL10-G556V | ||||||
Components | Mechanosensitive ion channel protein 10Mechanosensitive channels | ||||||
Keywords | TRANSPORT PROTEIN / ion channels / mechanosensitive channels / heptamer / Arabidopsis thaliana | ||||||
Function / homology | Function and homology information programmed cell death in response to reactive oxygen species / leaf senescence / detection of mechanical stimulus / mechanosensitive monoatomic ion channel activity / monoatomic anion transport / plasma membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Zhang, J. / Yuan, P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Open structure and gating of the Arabidopsis mechanosensitive ion channel MSL10. Authors: Jingying Zhang / Grigory Maksaev / Peng Yuan / Abstract: Plants are challenged by drastically different osmotic environments during growth and development. Adaptation to these environments often involves mechanosensitive ion channels that can detect and ...Plants are challenged by drastically different osmotic environments during growth and development. Adaptation to these environments often involves mechanosensitive ion channels that can detect and respond to mechanical force. In the model plant Arabidopsis thaliana, the mechanosensitive channel MSL10 plays a crucial role in hypo-osmotic shock adaptation and programmed cell death induction, but the molecular basis of channel function remains poorly understood. Here, we report a structural and electrophysiological analysis of MSL10. The cryo-electron microscopy structures reveal a distinct heptameric channel assembly. Structures of the wild-type channel in detergent and lipid environments, and in the absence of membrane tension, capture an open conformation. Furthermore, structural analysis of a non-conductive mutant channel demonstrates that reorientation of phenylalanine side chains alone, without main chain rearrangements, may generate the hydrophobic gate. Together, these results reveal a distinct gating mechanism and advance our understanding of mechanotransduction. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tdk.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8tdk.ent.gz | 732.7 KB | Display | PDB format |
PDBx/mmJSON format | 8tdk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/8tdk ftp://data.pdbj.org/pub/pdb/validation_reports/td/8tdk | HTTPS FTP |
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-Related structure data
Related structure data | 41165MC 8tdjC 8tdlC 8tdmC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.6019/EMPIAR-11614 / Data set type: EMPIAR / Details: EMPIAR-11614 |
-Links
-Assembly
Deposited unit |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 166 - 731 / Label seq-ID: 166 - 731
NCS oper:
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-Components
#1: Protein | Mass: 83997.641 Da / Num. of mol.: 7 / Mutation: G556V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MSL10 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q9LYG9 |
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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: AtMSL10 with mutation G556V / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Arabidopsis thaliana (thale cress) | ||||||||||||||||||||
Source (recombinant) | Organism: Komagataella pastoris (fungus) | ||||||||||||||||||||
Buffer solution | pH: 8 / Details: 20mM Tris-HCl PH 8.0, 150mM NaCl, and 0.04 mM GDN | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: AtMSL10-G556V in detergent | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 120000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Image recording | Electron dose: 44 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 3647 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1171913 | |||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C7 (7 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 376738 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | |||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8TDJ Accession code: 8TDJ / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 180.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS |
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