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- EMDB-34210: AtOSCA3.1 contracted state -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-34210
TitleAtOSCA3.1 contracted state
Map data
Sample
  • Complex: AtOSCA3.1 contracted state
    • Protein or peptide: CSC1-like protein ERD4
Keywordschannel / MEMBRANE PROTEIN
Function / homology
Function and homology information


plasmodesma / plant-type vacuole / chloroplast envelope / calcium-activated cation channel activity / mRNA binding / nucleus / plasma membrane
Similarity search - Function
Calcium permeable stress-gated cation channel 1-like / 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
CSC1-like protein ERD4
Similarity search - Component
Biological speciesArabidopsis (plant) / Arabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhang MF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: A mechanical-coupling mechanism in OSCA/TMEM63 channel mechanosensitivity.
Authors: Mingfeng Zhang / Yuanyue Shan / Charles D Cox / Duanqing Pei /
Abstract: Mechanosensitive (MS) ion channels are a ubiquitous type of molecular force sensor sensing forces from the surrounding bilayer. The profound structural diversity in these channels suggests that the ...Mechanosensitive (MS) ion channels are a ubiquitous type of molecular force sensor sensing forces from the surrounding bilayer. The profound structural diversity in these channels suggests that the molecular mechanisms of force sensing follow unique structural blueprints. Here we determine the structures of plant and mammalian OSCA/TMEM63 proteins, allowing us to identify essential elements for mechanotransduction and propose roles for putative bound lipids in OSCA/TMEM63 mechanosensation. Briefly, the central cavity created by the dimer interface couples each subunit and modulates dimeric OSCA/TMEM63 channel mechanosensitivity through the modulating lipids while the cytosolic side of the pore is gated by a plug lipid that prevents the ion permeation. Our results suggest that the gating mechanism of OSCA/TMEM63 channels may combine structural aspects of the 'lipid-gated' mechanism of MscS and TRAAK channels and the calcium-induced gating mechanism of the TMEM16 family, which may provide insights into the structural rearrangements of TMEM16/TMC superfamilies.
History
DepositionSep 2, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34210.png

Downloads & links

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Map

FileDownload / File: emd_34210.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.834 Å
Density
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.47430447 - 0.6951197
Average (Standard dev.)-0.0010234668 (±0.023875644)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34210_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34210_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AtOSCA3.1 contracted state

EntireName: AtOSCA3.1 contracted state
Components
  • Complex: AtOSCA3.1 contracted state
    • Protein or peptide: CSC1-like protein ERD4

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Supramolecule #1: AtOSCA3.1 contracted state

SupramoleculeName: AtOSCA3.1 contracted state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis (plant)

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Macromolecule #1: CSC1-like protein ERD4

MacromoleculeName: CSC1-like protein ERD4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 82.017727 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEFGSFLVSL GTSFVIFVIL MLLFTWLSRK SGNAPIYYPN RILKGLEPWE GTSLTRNPFA WMREALTSSE QDVVNLSGVD TAVHFVFLS TVLGIFACSS LLLLPTLLPL AATDNNIKNT KNATDTTSKG TFSQLDNLSM ANITKKSSRL WAFLGAVYWI S LVTYFFLW ...String:
MEFGSFLVSL GTSFVIFVIL MLLFTWLSRK SGNAPIYYPN RILKGLEPWE GTSLTRNPFA WMREALTSSE QDVVNLSGVD TAVHFVFLS TVLGIFACSS LLLLPTLLPL AATDNNIKNT KNATDTTSKG TFSQLDNLSM ANITKKSSRL WAFLGAVYWI S LVTYFFLW KAYKHVSSLR AQALMSADVK PEQFAILVRD MPAPPDGQTQ KEFIDSYFRE IYPETFYRSL VATENSKVNK IW EKLEGYK KKLARAEAIL AATNNRPTNK TGFCGLVGKQ VDSIEYYTEL INESVAKLET EQKAVLAEKQ QTAAVVFFTT RVA AASAAQ SLHCQMVDKW TVTEAPEPRQ LLWQNLNIKL FSRIIRQYFI YFFVAVTILF YMIPIAFVSA ITTLKNLQRI IPFI KPVVE ITAIRTVLES FLPQIALIVF LAMLPKLLLF LSKAEGIPSQ SHAIRAASGK YFYFSVFNVF IGVTLAGTLF NTVKD IAKN PKLDMIINLL ATSLPKSATF FLTYVALKFF IGYGLELSRI IPLIIFHLKK KYLCKTEAEV KEAWYPGDLS YATRVP GDM LILTITFCYS VIAPLILIFG ITYFGLGWLV LRNQALKVYV PSYESYGRMW PHIHQRILAA LFLFQVVMFG YLGAKTF FY TALVIPLIIT SLIFGYVCRQ KFYGGFEHTA LEVACRELKQ SPDLEEIFRA YIPHSLSSHK PEEHEFKGAM SRYQDFNA I AGV

UniProtKB: CSC1-like protein ERD4

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24872

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