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- EMDB-41044: Structure of mechanically activated ion channel OSCA2.3 in peptidiscs -

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Basic information

Entry
Database: EMDB / ID: EMD-41044
TitleStructure of mechanically activated ion channel OSCA2.3 in peptidiscs
Map dataOSCA2.3 in peptidisc postprocessed with LocalDeblur
Sample
  • Complex: OSCA2.3 in peptidisc
    • Protein or peptide: CSC1-like protein HYP1
  • Ligand: CHOLESTEROL
  • Ligand: PALMITIC ACID
Keywordsmechanically activated ion channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


mechanosensitive monoatomic ion channel activity / calcium-activated cation channel activity / 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
CSC1-like protein HYP1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsJojoa-Cruz S / Burendei B / Lee WH / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL143297 United States
CitationJournal: Structure / Year: 2024
Title: Structure of mechanically activated ion channel OSCA2.3 reveals mobile elements in the transmembrane domain.
Authors: Sebastian Jojoa-Cruz / Batuujin Burendei / Wen-Hsin Lee / Andrew B Ward /
Abstract: Members of the OSCA/TMEM63 family are mechanically activated ion channels and structures of some OSCA members have revealed the architecture of these channels and structural features that are ...Members of the OSCA/TMEM63 family are mechanically activated ion channels and structures of some OSCA members have revealed the architecture of these channels and structural features that are potentially involved in mechanosensation. However, these structures are all in a similar state and information about the motion of different elements of the structure is limited, preventing a deeper understanding of how these channels work. Here, we used cryoelectron microscopy to determine high-resolution structures of Arabidopsis thaliana OSCA1.2 and OSCA2.3 in peptidiscs. The structure of OSCA1.2 matches previous structures of the same protein in different environments. Yet, in OSCA2.3, the TM6a-TM7 linker adopts a different conformation that constricts the pore on its cytoplasmic side. Furthermore, coevolutionary sequence analysis uncovered a conserved interaction between the TM6a-TM7 linker and the beam-like domain (BLD). Our results reveal conformational heterogeneity and differences in conserved interactions between the TMD and BLD among members of the OSCA family.
History
DepositionJun 12, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41044.png

Downloads & links

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Map

FileDownload / File: emd_41044.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOSCA2.3 in peptidisc postprocessed with LocalDeblur
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 200 pix.
= 206. Å		1.03 Å/pix.
x 200 pix.
= 206. Å		1.03 Å/pix.
x 200 pix.
= 206. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0184
Minimum - Maximum-0.0033752986 - 0.16212064
Average (Standard dev.)0.00004148409 (±0.0038050876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 206.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: OSCA2.3 in peptidisc postprocessed with DeepEMhancer "highRes" model

Fileemd_41044_additional_1.map
AnnotationOSCA2.3 in peptidisc postprocessed with DeepEMhancer "highRes" model
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: OSCA2.3 in peptidisc half map 1

Fileemd_41044_half_map_1.map
AnnotationOSCA2.3 in peptidisc half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: OSCA2.3 in peptidisc half map 2

Fileemd_41044_half_map_2.map
AnnotationOSCA2.3 in peptidisc half 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 : OSCA2.3 in peptidisc

EntireName: OSCA2.3 in peptidisc
Components
  • Complex: OSCA2.3 in peptidisc
    • Protein or peptide: CSC1-like protein HYP1
  • Ligand: CHOLESTEROL
  • Ligand: PALMITIC ACID

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Supramolecule #1: OSCA2.3 in peptidisc

SupramoleculeName: OSCA2.3 in peptidisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 159 KDa

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Macromolecule #1: CSC1-like protein HYP1

MacromoleculeName: CSC1-like protein HYP1 / type: protein_or_peptide / ID: 1
Details: The last 10 residues (GTGTLEVLFQ) are leftover of a linker and protease site.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 80.848078 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLLSALLTSV GINLGLCFLF FTLYSILRKQ PSNVTVYGPR LVKKDGKSQQ SNEFNLERLL PTAGWVKRAL EPTNDEILSN LGLDALVFI RVFVFSIRVF SFASVVGIFI LLPVNYMGTE FEEFFDLPKK SMDNFSISNV NDGSNKLWIH FCAIYIFTAV V CSLLYYEH ...String:
MLLSALLTSV GINLGLCFLF FTLYSILRKQ PSNVTVYGPR LVKKDGKSQQ SNEFNLERLL PTAGWVKRAL EPTNDEILSN LGLDALVFI RVFVFSIRVF SFASVVGIFI LLPVNYMGTE FEEFFDLPKK SMDNFSISNV NDGSNKLWIH FCAIYIFTAV V CSLLYYEH KYILTKRIAH LYSSKPQPQE FTVLVSGVPL VSGNSISETV ENFFREYHSS SYLSHIVVHR TDKLKVLMND AE KLYKKLT RVKSGSISRQ KSRWGGFLGM FGNNVDVVDH YQKKLDKLED DMRLKQSLLA GEEVPAAFVS FRTRHGAAIA TNI QQGIDP TQWLTEAAPE PEDVHWPFFT ASFVRRWISN VVVLVAFVAL LILYIVPVVL VQGLANLHQL ETWFPFLKGI LNMK IVSQV ITGYLPSLIF QLFLLIVPPI MLLLSSMQGF ISHSQIEKSA CIKLLIFTVW NSFFANVLSG SALYRVNVFL EPKTI PRVL AAAVPAQASF FVSYVVTSGW TGLSSEILRL VPLLWSFITK LFGKEDDKEF EVPSTPFCQE IPRILFFGLL GITYFF LSP LILPFLLVYY CLGYIIYRNQ LLNVYAAKYE TGGKFWPIVH SYTIFSLVLM HIIAVGLFGL KELPVASSLT IPLPVLT VL FSIYCQRRFL PNFKSYPTQC LVNKDKADER EQNMSEFYSE LVVAYRDPAL SASQDSRDIS PGTGTLEVLF Q

UniProtKB: CSC1-like protein HYP1

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Macromolecule #2: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 4 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #3: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 3 / Number of copies: 16 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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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

Concentration3.6 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
25.0 mMTris
150.0 mMsodium chlorideNaCl
2.0 mMdithiothreitol
GridMaterial: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
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: 3 / Number real images: 5323 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 29000
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

Particle selectionNumber selected: 2683410
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 180640
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6mgv


Chain - Chain ID: A / Chain - Source name: SwissModel / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8t57:
Structure of mechanically activated ion channel OSCA2.3 in peptidiscs

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