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Yorodumi- EMDB-20017: Structure of the rice hyperosmolality-gated ion channel OSCA1.2 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20017 | |||||||||
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Title | Structure of the rice hyperosmolality-gated ion channel OSCA1.2 | |||||||||
Map data | rice hyperosmolality-gated ion channel OSCA1.2 | |||||||||
Sample |
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Keywords | ion channel osmolality gated / TRANSPORT PROTEIN | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 4.9 Å | |||||||||
Authors | Maity K / Heumann JM | |||||||||
Funding support | United States, 2 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20017.map.gz | 49.2 MB | EMDB map data format | |
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Header (meta data) | emd-20017-v30.xml emd-20017.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
Images | emd_20017.png | 183.5 KB | ||
Filedesc metadata | emd-20017.cif.gz | 6.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20017 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20017 | HTTPS FTP |
-Validation report
Summary document | emd_20017_validation.pdf.gz | 664.8 KB | Display | EMDB validaton report |
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Full document | emd_20017_full_validation.pdf.gz | 664.4 KB | Display | |
Data in XML | emd_20017_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_20017_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20017 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20017 | HTTPS FTP |
-Related structure data
Related structure data | 6oceMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20017.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | rice hyperosmolality-gated ion channel OSCA1.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : OSCA1.2 dimer
Entire | Name: OSCA1.2 dimer |
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Components |
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-Supramolecule #1: OSCA1.2 dimer
Supramolecule | Name: OSCA1.2 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Oryza sativa subsp. japonica (Japanese rice) |
Molecular weight | Theoretical: 180 KDa |
-Macromolecule #1: stress-gated cation channel 1.2
Macromolecule | Name: stress-gated cation channel 1.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryza sativa subsp. japonica (Japanese rice) |
Molecular weight | Theoretical: 88.876383 KDa |
Recombinant expression | Organism: Komagataella pastoris (fungus) |
Sequence | String: MATVSDIGLS AAINVSMAVA FLLVFAFLRL QPINDRVYFP KWYLRGMRDS PVSSGAAVQK VVNLNMRSYL KFLSWMPAAL KMPEDELIN HAGLDSAVYL RIYLTGIKIF VPISILASLV LFPVNWTNDT LDSMKVVHSK IDKLSISNIP YGSNRFVTHL V MAYAVTFW ...String: MATVSDIGLS AAINVSMAVA FLLVFAFLRL QPINDRVYFP KWYLRGMRDS PVSSGAAVQK VVNLNMRSYL KFLSWMPAAL KMPEDELIN HAGLDSAVYL RIYLTGIKIF VPISILASLV LFPVNWTNDT LDSMKVVHSK IDKLSISNIP YGSNRFVTHL V MAYAVTFW TCYVLFREYE IITTMRLRFL ASEKRRPDQF TVLVRNIPPD PDESISELVE HFFLVNHPDH YLRHQVVYNA NK LADLVEK KKKLQNWLDY YQLKYERNPS KRPTTKTGFL GCFGSEVDAI EYYKAEIEKI GKEEADERQK IMKDPQSAVP AAF VSFRSR WGAAVCAQTQ QTSNPTVWIT EWAPEPRDVY WNNLSIPFVS LTVRRLIVAV AFFFLNFFYV IPIAFVQSLA SLEG IEKAL PFLKPLIKID VIKSFIQGFL PGIALKVFLI LLPTILMFMS KFEGLISQSS LERRSASKYY IFLFFNVFLG SIVTG SALD QLKAYIHQSA NEIPRTIGVA IPMRATFFIT YVMVDGWTGV AGEILRLRAL IIFHLKNFFL VKTEKDREEA MDPGSI CFD WCEPRIQLYF LLGLVYAVVT PLLLPFILVF FGLAYVVYRH QIINVYNQQY ESGAQFWPSV HGRIIIALIV SQLLLIG LL STKGFEETTP VLVVLPVLTF WFYKYCKNRF EPAFVRNPLQ EAMRKDTLER AREPTFDLKA YLANAYLHPV FKGREEED N MSISEDVGME EVIVPTKRQS RRNTPAQSKY EGSDTLSLPE TVHERIKPQL EGS UniProtKB: Os05g0594700 protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: unspecified | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 5 / Number real images: 2408 / Average exposure time: 1.0 sec. / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 400 |
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Output model | PDB-6oce: |