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- EMDB-39403: OSCA1.1-F516A nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-39403
TitleOSCA1.1-F516A nanodisc
Map data
Sample
  • Complex: OSCA1.1-F516A pre-open 1
    • Protein or peptide: Protein OSCA1
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
KeywordsOSCA1.1-F516A nanodisc / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of calcium ion import / calcium-activated cation channel activity / cellular hyperosmotic response / response to osmotic stress / monoatomic cation channel activity / protein tetramerization / plasma membrane / cytosol
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
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsZhang MF
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: Nat Commun / Year: 2024
Title: Activation mechanisms of dimeric mechanosensitive OSCA/TMEM63 channels.
Authors: Yuanyue Shan / Mengmeng Zhang / Meiyu Chen / Xinyi Guo / Ying Li / Mingfeng Zhang / Duanqing Pei /
Abstract: OSCA/TMEM63 channels, which have transporter-like architectures, are bona fide mechanosensitive (MS) ion channels that sense high-threshold mechanical forces in eukaryotic cells. The activation ...OSCA/TMEM63 channels, which have transporter-like architectures, are bona fide mechanosensitive (MS) ion channels that sense high-threshold mechanical forces in eukaryotic cells. The activation mechanism of these transporter-like channels is not fully understood. Here we report cryo-EM structures of a dimeric OSCA/TMEM63 pore mutant OSCA1.1-F516A with a sequentially extracellular dilated pore in a detergent environment. These structures suggest that the extracellular pore sequential dilation resembles a flower blooming and couples to a sequential contraction of each monomer subunit towards the dimer interface and subsequent extrusion of the dimer interface lipids. Interestingly, while OSCA1.1-F516A remains non-conducting in the native lipid environment, it can be directly activated by lyso-phosphatidylcholine (Lyso-PC) with reduced single-channel conductance. Structural analysis of OSCA1.1-F516A in lyso-PC-free and lyso-PC-containing lipid nanodiscs indicates that lyso-PC induces intracellular pore dilation by attracting the M6b to upward movement away from the intracellular side thus extending the intracellular pore. Further functional studies indicate that full activation of MS OSCA/TMEM63 dimeric channels by high-threshold mechanical force also involves the opening of both intercellular and extracellular pores. Our results provide the fundamental activation paradigm of the unique transporter-like MS OSCA/TMEM63 channels, which is likely applicable to functional branches of the TMEM63/TMEM16/TMC superfamilies.
History
DepositionMar 9, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39403.png

Downloads & links

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Map

FileDownload / File: emd_39403.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 512 pix.
= 291.84 Å		0.57 Å/pix.
x 512 pix.
= 291.84 Å		0.57 Å/pix.
x 512 pix.
= 291.84 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.57 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.37259898 - 0.6415229
Average (Standard dev.)0.00022418014 (±0.016031444)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 291.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39403_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Half map: #1

Fileemd_39403_half_map_2.map
Projections & Slices
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Sample components

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Entire : OSCA1.1-F516A pre-open 1

EntireName: OSCA1.1-F516A pre-open 1
Components
  • Complex: OSCA1.1-F516A pre-open 1
    • Protein or peptide: Protein OSCA1
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

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Supramolecule #1: OSCA1.1-F516A pre-open 1

SupramoleculeName: OSCA1.1-F516A pre-open 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Protein OSCA1

MacromoleculeName: Protein OSCA1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 87.620914 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATLKDIGVS AGINILTAFI FFIIFAFLRL QPFNDRVYFS KWYLRGLRSS PASGGGFAGR FVNLELRSYL KFLHWMPEAL KMPERELID HAGLDSVVYL RIYWLGLKIF APIAMLAWAV LVPVNWTNNE LELAKHFKNV TSSDIDKLTI SNIPEGSNRF W AHIIMAYA ...String:
MATLKDIGVS AGINILTAFI FFIIFAFLRL QPFNDRVYFS KWYLRGLRSS PASGGGFAGR FVNLELRSYL KFLHWMPEAL KMPERELID HAGLDSVVYL RIYWLGLKIF APIAMLAWAV LVPVNWTNNE LELAKHFKNV TSSDIDKLTI SNIPEGSNRF W AHIIMAYA FTIWTCYMLM KEYETVANMR LQFLASEGRR PDQFTVLVRN VPPDPDETVS ELVEHFFLVN HPDNYLTHQV VC NANKLAD LVSKKTKLQN WLDYYQLKYT RNNSQIRPIT KLGCLGLCGQ KVDAIEHYIA EVDKTSKEIA EERENVVNDQ KSV MPASFV SFKTRWAAAV CAQTTQTRNP TEWLTEWAAE PRDIYWPNLA IPYVSLTVRR LVMNVAFFFL TFFFIIPIAF VQSL ATIEG IEKVAPFLKV IIEKDFIKSL IQGLLAGIAL KLFLIFLPAI LMTMSKFEGF TSVSFLERRS ASRYYIFNLV NVFLG SVIA GAAFEQLNSF LNQSPNQIPK TIGMAIPMKA TAFITYIMVD GWAGVAGEIL MLKPLIIYHL KNAFLVKTEK DREEAM NPG SIGFNTGEPQ IQLYFLLGLV YAPVTPMLLP FILVFFALAY VVYRHQIINV YNQEYESAAA FWPDVHGRVI TALIISQ LL LMGLLGTKHA ASAAPFLIAL PVITIGFHRF CKGRFEPAFV RYPLQEAMMK DTLERAREPN LNLKGYLQDA YIHPVFKG G DNDDDGDMIG KLENEVIIVP TKRQSRRNTP APSRISGESS PSLAVINGKE V

UniProtKB: Protein OSCA1

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Macromolecule #2: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 2 / Number of copies: 4 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 60000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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