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- PDB-6ijz: Structure of a plant cation channel -

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Basic information

Entry
Database: PDB / ID: 6ijz
TitleStructure of a plant cation channel
ComponentsCalcium permeable stress-gated cation channel 1
KeywordsMEMBRANE PROTEIN / Channel
Function / homology
Function and homology information


mechanosensitive monoatomic ion channel activity / calcium-activated cation channel activity / monoatomic cation transport / identical protein binding / plasma membrane
Similarity search - Function
CSC1/OSCA1-like, 7TM region / CSC1/OSCA1-like, cytosolic domain / CSC1/OSCA1-like, N-terminal transmembrane domain / Calcium permeable stress-gated cation channel 1-like / Calcium-dependent channel, 7TM region, putative phosphate / Late exocytosis, associated with Golgi transport / Cytosolic domain of 10TM putative phosphate transporter
Similarity search - Domain/homology
Hyperosmolality-gated Ca2+ permeable channel 1.2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsSun, L. / Wang, J. / Liu, X.
Funding support China, 2items
OrganizationGrant numberCountry
KY2070000059 China
2015CB910104 China
CitationJournal: Nat Commun / Year: 2018
Title: Structure of the hyperosmolality-gated calcium-permeable channel OSCA1.2.
Authors: Xin Liu / Jiawei Wang / Linfeng Sun /
Abstract: In plants, hyperosmolality stimuli triggers opening of the osmosensitive channels, leading to a rapid downstream signaling cascade initiated by cytosolic calcium concentration elevation. Members of ...In plants, hyperosmolality stimuli triggers opening of the osmosensitive channels, leading to a rapid downstream signaling cascade initiated by cytosolic calcium concentration elevation. Members of the OSCA family in Arabidopsis thaliana, identified as the hyperosmolality-gated calcium-permeable channels, have been suggested to play a key role during the initial phase of hyperosmotic stress response. Here, we report the atomic structure of Arabidopsis OSCA1.2 determined by single-particle cryo-electron microscopy. It contains 11 transmembrane helices and forms a homodimer. It is in an inactivated state, and the pore-lining residues are clearly identified. Its cytosolic domain contains a RNA recognition motif and two unique long helices. The linker between these two helices forms an anchor in the lipid bilayer and may be essential to osmosensing. The structure of AtOSCA1.2 serves as a platform for the study of the mechanism underlying osmotic stress responses and mechanosensing.
History
DepositionOct 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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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Structure visualization

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Assembly

Deposited unit
A: Calcium permeable stress-gated cation channel 1
B: Calcium permeable stress-gated cation channel 1


Theoretical massNumber of molelcules
Total (without water)175,9712
Polymers175,9712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2530 Å2
ΔGint-10 kcal/mol
Surface area62870 Å2

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Components

#1: Protein Calcium permeable stress-gated cation channel 1 / Plant cation channel / AtCSC1


Mass: 87985.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CSC1, At4g22120, F1N20.220 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5XEZ5

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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: Plant chennel / Type: CELL
Details: Protein expressed in Sf-9 cell and purified in digitonin
Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K / Details: blot for 4 seconds before plunging

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 32

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
1RELION2particle selection
2UCSFImage4image acquisition
4GctfCTF correction
9RELION2initial Euler assignment
10RELION2final Euler assignment
11RELION2classification
12RELION23D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 271802 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00811272
ELECTRON MICROSCOPYf_angle_d1.115348
ELECTRON MICROSCOPYf_dihedral_angle_d9.7256646
ELECTRON MICROSCOPYf_chiral_restr0.0641744
ELECTRON MICROSCOPYf_plane_restr0.0091914

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