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- PDB-6oce: Structure of the rice hyperosmolality-gated ion channel OSCA1.2 -

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Basic information

Entry
Database: PDB / ID: 6oce
TitleStructure of the rice hyperosmolality-gated ion channel OSCA1.2
Componentsstress-gated cation channel 1.2
KeywordsTRANSPORT PROTEIN / ion channel osmolality gated
Function / homology
Function and homology information


calcium-activated cation channel activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
CSC1/OSCA1-like, 7TM region / CSC1/OSCA1-like, cytosolic domain / CSC1/OSCA1-like, N-terminal transmembrane domain / Calcium-dependent channel, 7TM region, putative phosphate / Late exocytosis, associated with Golgi transport / Cytosolic domain of 10TM putative phosphate transporter
Similarity search - Domain/homology
Os05g0594700 protein
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsMaity, K. / Heumann, J.M. / McGrath, A.P. / Chang, G. / Stowell, M.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)PGRP IOS-1444435 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM116789 United States
CitationJournal: 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
DepositionMar 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: stress-gated cation channel 1.2
B: stress-gated cation channel 1.2


Theoretical massNumber of molelcules
Total (without water)177,7532
Polymers177,7532
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2150 Å2
ΔGint-10 kcal/mol
Surface area82820 Å2

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Components

#1: Protein stress-gated cation channel 1.2 / Os05g0594700 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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: OSCA1.2 dimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.18 MDa / Experimental value: YES
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)
Source (recombinant)Organism: Komagataella pastoris (fungus)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
10.01 %cholesteryl hemisuccinateC31H50O41
20.06 %n-undecyl-beta-D-maltopyranosideC23H44O111
3150 mMsodium chlorideNaClSodium chloride1
420 mMHEPESC8H18N2O4S1
50.2 mMTCEPC9H15O6P1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus min: 500 nm / Cs: 2.2 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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 opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV / Phase plate: VOLTA PHASE PLATE
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategory
1RELION2particle selection
2Leginonimage acquisition
7PHENIXmodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11RELIONfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 169655
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64096 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 400 / Protocol: AB INITIO MODEL / Space: REAL

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