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- EMDB-9677: Cryo-EM single particle analysis of a cation channel -

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Basic information

Entry
Database: EMDB / ID: EMD-9677
TitleCryo-EM single particle analysis of a cation channel
Map dataEM map of a plant hyperosmolality-gated calcium-permeable channel, AtOSCA2.2
Sample
  • Cell: Plant chennel
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
Calcium permeable stress-gated cation channel 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsSun L / Wang J / Liu X
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 10, 2018-
Header (metadata) releaseDec 12, 2018-
Map releaseDec 12, 2018-
UpdateDec 12, 2018-
Current statusDec 12, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.031
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.031
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9677.png

Downloads & links

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Map

FileDownload / File: emd_9677.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of a plant hyperosmolality-gated calcium-permeable channel, AtOSCA2.2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.031
Minimum - Maximum-0.043955125 - 0.09801195
Average (Standard dev.)0.0017512817 (±0.007216753)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z208.000208.000208.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0440.0980.002

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Supplemental data

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Sample components

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Entire : Plant chennel

EntireName: Plant chennel
Components
  • Cell: Plant chennel

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Supramolecule #1: Plant chennel

SupramoleculeName: Plant chennel / type: cell / ID: 1 / Parent: 0
Details: Protein expressed in Sf-9 cell and purified in digitonin
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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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

Concentration5 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4 seconds before plunging.
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 8.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 123777
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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