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- PDB-8t56: Structure of mechanically activated ion channel OSCA1.2 in peptidiscs -

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Basic information

Entry
Database: PDB / ID: 8t56
TitleStructure of mechanically activated ion channel OSCA1.2 in peptidiscs
Components
  • Calcium permeable stress-gated cation channel 1
  • NSPr peptide
KeywordsMEMBRANE PROTEIN / mechanically activated ion channel
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
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
CHOLESTEROL / 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / PALMITIC ACID / CHOLESTEROL HEMISUCCINATE / Calcium permeable stress-gated cation channel 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsBurendei, B. / Jojoa-Cruz, S. / Lee, W.H. / Ward, A.B.
Funding support United States, 1items
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, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calcium permeable stress-gated cation channel 1
B: Calcium permeable stress-gated cation channel 1
C: NSPr peptide
D: NSPr peptide
E: NSPr peptide
F: NSPr peptide
G: NSPr peptide
H: NSPr peptide
I: NSPr peptide
J: NSPr peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,40146
Polymers213,92010
Non-polymers11,48136
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein / Protein/peptide , 2 types, 10 molecules ABCDEFGHIJ

#1: Protein Calcium permeable stress-gated cation channel 1 / AtCSC1


Mass: 89031.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The last 10 residues (GTGTLEVLFQ) are leftover of a linker and protease site.
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CSC1, At4g22120, F1N20.220 / Plasmid: pcDNA3.1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q5XEZ5
#2: Protein/peptide
NSPr peptide


Mass: 4482.132 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: Synthesized by Peptidisc Biotech / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 36 molecules

#3: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H50O4
#4: Chemical...
ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical ChemComp-LBN / 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / (2R)-2-[(9Z)-9-Octadecenoyloxy]-3-(palmitoyloxy)propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#6: Chemical
ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H46O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1OSCA1.2 in peptidiscCOMPLEX#1-#20MULTIPLE SOURCES
2OSCA1.2COMPLEX#11RECOMBINANT
3peptidisc peptideCOMPLEX#21SYNTHETIC
Molecular weightValue: 0.176 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Arabidopsis thaliana (thale cress)3702
33synthetic construct (others)32630
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293F / Plasmid: pcDNA3.1
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTris1
2150 mMsodium chlorideNaClSodium chloride1
32 mMdithiothreitol1
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 29000 X / Nominal defocus max: 1400 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1805
Image scansWidth: 3710 / Height: 3838 / Movie frames/image: 36

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Processing

EM software
IDNameVersionCategoryDetails
2Leginonimage acquisition
4Gctf1.06CTF correctionFor CryoSPARC
7Coot0.9model fitting
9cryoSPARC2initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13Coot0.9model refinement
14PHENIX1.18.2-3874model refinement
15Rosetta3.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1046049
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52250 / Details: SIDESPLITTER was used for reconstruction step / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6MGV

6mgv


Accession code: 6MGV / Source name: PDB / Type: experimental model

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