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- EMDB-20017: Structure of the rice hyperosmolality-gated ion channel OSCA1.2 -

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Basic information

Entry
Database: EMDB / ID: EMD-20017
TitleStructure of the rice hyperosmolality-gated ion channel OSCA1.2
Map datarice hyperosmolality-gated ion channel OSCA1.2
Sample
  • Complex: OSCA1.2 dimer
    • Protein or peptide: stress-gated cation channel 1.2
Keywordsion channel osmolality gated / TRANSPORT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsMaity K / Heumann JM
Funding support United States, 2 items
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, 2019-
Header (metadata) releaseApr 17, 2019-
Map releaseJul 3, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6oce
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20017.png

Downloads & links

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Map

FileDownload / File: emd_20017.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrice hyperosmolality-gated ion channel OSCA1.2
Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.035
Minimum - Maximum-0.051807053 - 0.09677975
Average (Standard dev.)0.00006969964 (±0.005749823)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 331.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z331.200331.200331.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ254265109
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0520.0970.000

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Supplemental data

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Sample components

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Entire : OSCA1.2 dimer

EntireName: OSCA1.2 dimer
Components
  • Complex: OSCA1.2 dimer
    • Protein or peptide: stress-gated cation channel 1.2

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Supramolecule #1: OSCA1.2 dimer

SupramoleculeName: OSCA1.2 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)
Molecular weightTheoretical: 180 KDa

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Macromolecule #1: stress-gated cation channel 1.2

MacromoleculeName: stress-gated cation channel 1.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)
Molecular weightTheoretical: 88.876383 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
0.01 %C31H50O4cholesteryl hemisuccinate
0.06 %C23H44O11n-undecyl-beta-D-maltopyranoside
150.0 mMNaClSodium chloridesodium chloride
20.0 mMC8H18N2O4SHEPES
0.2 mMC9H15O6PTCEP
GridSupport film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus min: 0.5 µm
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 169655
Startup modelType of model: NONE
Initial angle assignmentType: COMMON LINE / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 1
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 64096

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 400
Output model

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

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