+Open data
-Basic information
Entry | Database: PDB / ID: 6oce | |||||||||
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Title | Structure of the rice hyperosmolality-gated ion channel OSCA1.2 | |||||||||
Components | stress-gated cation channel 1.2 | |||||||||
Keywords | TRANSPORT PROTEIN / ion channel osmolality gated | |||||||||
Function / homology | Function and homology information calcium-activated cation channel activity / membrane => GO:0016020 / plasma membrane Similarity search - Function | |||||||||
Biological species | Oryza sativa subsp. japonica (Japanese rice) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å | |||||||||
Authors | Maity, K. / Heumann, J.M. / McGrath, A.P. / Chang, G. / Stowell, M.H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: Cryo-EM structure of OSCA1.2 from elucidates the mechanical basis of potential membrane hyperosmolality gating. Authors: Koustav Maity / John M Heumann / Aaron P McGrath / Noah J Kopcho / Po-Kai Hsu / Chang-Wook Lee / James H Mapes / Denisse Garza / Srinivasan Krishnan / Garry P Morgan / Kevin J Hendargo / ...Authors: Koustav Maity / John M Heumann / Aaron P McGrath / Noah J Kopcho / Po-Kai Hsu / Chang-Wook Lee / James H Mapes / Denisse Garza / Srinivasan Krishnan / Garry P Morgan / Kevin J Hendargo / Thomas Klose / Steven D Rees / Arturo Medrano-Soto / Milton H Saier / Miguel Piñeros / Elizabeth A Komives / Julian I Schroeder / Geoffrey Chang / Michael H B Stowell / Abstract: Sensing and responding to environmental water deficiency and osmotic stresses are essential for the growth, development, and survival of plants. Recently, an osmolality-sensing ion channel called ...Sensing and responding to environmental water deficiency and osmotic stresses are essential for the growth, development, and survival of plants. Recently, an osmolality-sensing ion channel called OSCA1 was discovered that functions in sensing hyperosmolality in Here, we report the cryo-electron microscopy (cryo-EM) structure and function of an OSCA1 homolog from rice (; OsOSCA1.2), leading to a model of how it could mediate hyperosmolality sensing and transport pathway gating. The structure reveals a dimer; the molecular architecture of each subunit consists of 11 transmembrane (TM) helices and a cytosolic soluble domain that has homology to RNA recognition proteins. The TM domain is structurally related to the TMEM16 family of calcium-dependent ion channels and lipid scramblases. The cytosolic soluble domain possesses a distinct structural feature in the form of extended intracellular helical arms that are parallel to the plasma membrane. These helical arms are well positioned to potentially sense lateral tension on the inner leaflet of the lipid bilayer caused by changes in turgor pressure. Computational dynamic analysis suggests how this domain couples to the TM portion of the molecule to open a transport pathway. Hydrogen/deuterium exchange mass spectrometry (HDXMS) experimentally confirms the conformational dynamics of these coupled domains. These studies provide a framework to understand the structural basis of proposed hyperosmolality sensing in a staple crop plant, extend our knowledge of the anoctamin superfamily important for plants and fungi, and provide a structural mechanism for potentially translating membrane stress to transport regulation. | |||||||||
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 | 6oce.cif.gz | 250.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oce.ent.gz | 204.2 KB | Display | PDB format |
PDBx/mmJSON format | 6oce.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oce_validation.pdf.gz | 1009 KB | Display | wwPDB validaton report |
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Full document | 6oce_full_validation.pdf.gz | 1022.4 KB | Display | |
Data in XML | 6oce_validation.xml.gz | 41.6 KB | Display | |
Data in CIF | 6oce_validation.cif.gz | 61.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/6oce ftp://data.pdbj.org/pub/pdb/validation_reports/oc/6oce | HTTPS FTP |
-Related structure data
Related structure data | 20017MC 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: 88876.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: Os05g0594700, OSJNBa0030I14.5, OSNPB_050594700 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q5TKG1 |
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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: OSCA1.2 dimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.18 MDa / Experimental value: YES | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Oryza sativa subsp. japonica (Japanese rice) | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Komagataella pastoris (fungus) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Details: unspecified | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 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 FIELD / Nominal defocus min: 500 nm / Cs: 2.2 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1 sec. / Electron dose: 55 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 5 / Num. of real images: 2408 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV / Phase plate: VOLTA PHASE PLATE |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 169655 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64096 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | B value: 400 / Protocol: AB INITIO MODEL / Space: REAL |