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- EMDB-9112: Cryo-EM map of mechanically activated ion channel OSCA1.2 in nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-9112
TitleCryo-EM map of mechanically activated ion channel OSCA1.2 in nanodisc
Map dataCryo-EM map of mechanically activated ion channel OSCA1.2 in nanodisc
Sample
  • Organelle or cellular component: OSCA1.2
    • Protein or peptide: Calcium permeable stress-gated cation channel 1
KeywordsMechanically activated ion channel / MEMBRANE PROTEIN
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: 3.1 Å
AuthorsJojoa-Cruz S / Saotome K
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1R35NS105067 United States
CitationJournal: Elife / Year: 2018
Title: Cryo-EM structure of the mechanically activated ion channel OSCA1.2.
Authors: Sebastian Jojoa-Cruz / Kei Saotome / Swetha E Murthy / Che Chun Alex Tsui / Mark Sp Sansom / Ardem Patapoutian / Andrew B Ward /
Abstract: Mechanically activated ion channels underlie touch, hearing, shear-stress sensing, and response to turgor pressure. OSCA/TMEM63s are a newly-identified family of eukaryotic mechanically activated ion ...Mechanically activated ion channels underlie touch, hearing, shear-stress sensing, and response to turgor pressure. OSCA/TMEM63s are a newly-identified family of eukaryotic mechanically activated ion channels opened by membrane tension. The structural underpinnings of OSCA/TMEM63 function are not explored. Here, we elucidate high resolution cryo-electron microscopy structures of OSCA1.2, revealing a dimeric architecture containing eleven transmembrane helices per subunit and surprising topological similarities to TMEM16 proteins. We locate the ion permeation pathway within each subunit by demonstrating that a conserved acidic residue is a determinant of channel conductance. Molecular dynamics simulations reveal membrane interactions, suggesting the role of lipids in OSCA1.2 gating. These results lay a foundation to decipher how the structural organization of OSCA/TMEM63 is suited for their roles as MA ion channels.
History
DepositionSep 15, 2018-
Header (metadata) releaseOct 10, 2018-
Map releaseNov 14, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0728
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0728
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6mgv
  • Surface level: 0.0728
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9112.png

Downloads & links

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Map

FileDownload / File: emd_9112.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of mechanically activated ion channel OSCA1.2 in nanodisc
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 200 pix.
= 230. Å		1.15 Å/pix.
x 200 pix.
= 230. Å		1.15 Å/pix.
x 200 pix.
= 230. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0728 / Movie #1: 0.0728
Minimum - Maximum-0.3785452 - 0.73091245
Average (Standard dev.)0.00006264082 (±0.020847335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 230.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z230.000230.000230.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.3790.7310.000

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Supplemental data

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Half map: Half map 1

Fileemd_9112_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_9112_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : OSCA1.2

EntireName: OSCA1.2
Components
  • Organelle or cellular component: OSCA1.2
    • Protein or peptide: Calcium permeable stress-gated cation channel 1

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Supramolecule #1: OSCA1.2

SupramoleculeName: OSCA1.2 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 88 KDa

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Macromolecule #1: Calcium permeable stress-gated cation channel 1

MacromoleculeName: Calcium permeable stress-gated cation channel 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 89.031719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATLQDIGVS AGINILSAFV FFIIFAVLRL QPFNDRVYFS KWYLKGLRSS PARGGAFAQR FVNLDFRSYM KFLNWMPEAL KMPEPELID HAGLDSVVYL RIYWLGLKIF TPIAVLAWAV LVPVNWTNNT LEMAKQLRNV TSSDIDKLSV SNIPEYSMRF W THIVMAYA ...String:
MATLQDIGVS AGINILSAFV FFIIFAVLRL QPFNDRVYFS KWYLKGLRSS PARGGAFAQR FVNLDFRSYM KFLNWMPEAL KMPEPELID HAGLDSVVYL RIYWLGLKIF TPIAVLAWAV LVPVNWTNNT LEMAKQLRNV TSSDIDKLSV SNIPEYSMRF W THIVMAYA FTIWTCYVLM KEYETIANMR LQFVASEARR PDQFTVLVRN VPPDADESVS ELVEHFFLVN HPDHYLTHQV VC NANKLAD LVKKKKKLQN WLDYYQLKYA RNNSQRIMVK LGFLGLWGQK VDAIEHYIAE IDKISKEISK EREEVVNDPK AIM PAAFVS FKTRWAAAVC AQTQQTRNPT QWLTEWAPEP RDVFWSNLAI PYVSLTVRRL IMHVAFFFLT FFFIVPIAFV QSLA TIEGI VKAAPFLKFI VDDKFMKSVI QGFLPGIALK LFLAFLPSIL MIMSKFEGFT SISSLERRAA FRYYIFNLVN VFLAS VIAG AAFEQLNSFL NQSANQIPKT IGVAIPMKAT FFITYIMVDG WAGVAGEILM LKPLIMFHLK NAFLVKTDKD REEAMD PGS IGFNTGEPRI QLYFLLGLVY APVTPMLLPF ILVFFALAYI VYRHQIINVY NQEYESAAAF WPDVHGRVIA ALVISQL LL MGLLGTKHAA LAAPFLIALP VLTIGFHHFC KGRYEPAFIR YPLQEAMMKD TLETAREPNL NLKGYLQNAY VHPVFKGD E DDYDIDDKLG KFEDEAIIVP TKRQSRRNTP APSIISGDDS PSLPFSGKLV GTGTLEVLFQ

UniProtKB: Calcium permeable stress-gated cation channel 1

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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

Concentration2.1 mg/mL
BufferpH: 8
GridMaterial: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Number grids imaged: 1 / Number real images: 1740 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.2 µm / Nominal defocus min: -0.4 µm / Nominal magnification: 36000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 326398
Startup modelType of model: NONE
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 76797
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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