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- PDB-8xry: Cryo-EM structure of OSCA3.1-1.1ver(Y367N-G454S-Y458I)-open/open state -

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Basic information

Entry
Database: PDB / ID: 8xry
TitleCryo-EM structure of OSCA3.1-1.1ver(Y367N-G454S-Y458I)-open/open state
ComponentsCSC1-like protein ERD4
KeywordsPLANT PROTEIN / OSCA/TMEM63 channel / mechanosensitive channel
Function / homology
Function and homology information


plant-type vacuole / plasmodesma / chloroplast envelope / calcium-activated cation channel activity / mRNA binding / nucleus / 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
CSC1-like protein ERD4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.84 Å
AuthorsZhang, Y. / Han, Y.
Funding support China, Australia, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022ZD0207400 China
Australian Research Council (ARC)FT220100159 Australia
Australian Research Council (ARC)DP200100860 Australia
CitationJournal: Nature / Year: 2024
Title: Mechanical activation opens a lipid-lined pore in OSCA ion channels.
Authors: Yaoyao Han / Zijing Zhou / Ruitao Jin / Fei Dai / Yifan Ge / Xisan Ju / Xiaonuo Ma / Sitong He / Ling Yuan / Yingying Wang / Wei Yang / Xiaomin Yue / Zhongwen Chen / Yadong Sun / Ben Corry / ...Authors: Yaoyao Han / Zijing Zhou / Ruitao Jin / Fei Dai / Yifan Ge / Xisan Ju / Xiaonuo Ma / Sitong He / Ling Yuan / Yingying Wang / Wei Yang / Xiaomin Yue / Zhongwen Chen / Yadong Sun / Ben Corry / Charles D Cox / Yixiao Zhang /
Abstract: OSCA/TMEM63 channels are the largest known family of mechanosensitive channels, playing critical roles in plant and mammalian mechanotransduction. Here we determined 44 cryogenic electron microscopy ...OSCA/TMEM63 channels are the largest known family of mechanosensitive channels, playing critical roles in plant and mammalian mechanotransduction. Here we determined 44 cryogenic electron microscopy structures of OSCA/TMEM63 channels in different environments to investigate the molecular basis of OSCA/TMEM63 channel mechanosensitivity. In nanodiscs, we mimicked increased membrane tension and observed a dilated pore with membrane access in one of the OSCA1.2 subunits. In liposomes, we captured the fully open structure of OSCA1.2 in the inside-in orientation, in which the pore shows a large lateral opening to the membrane. Unusually for ion channels, structural, functional and computational evidence supports the existence of a 'proteo-lipidic pore' in which lipids act as a wall of the ion permeation pathway. In the less tension-sensitive homologue OSCA3.1, we identified an 'interlocking' lipid tightly bound in the central cleft, keeping the channel closed. Mutation of the lipid-coordinating residues induced OSCA3.1 activation, revealing a conserved open conformation of OSCA channels. Our structures provide a global picture of the OSCA channel gating cycle, uncover the importance of bound lipids and show that each subunit can open independently. This expands both our understanding of channel-mediated mechanotransduction and channel pore formation, with important mechanistic implications for the TMEM16 and TMC protein families.
History
DepositionJan 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed
Revision 1.2May 8, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CSC1-like protein ERD4
B: CSC1-like protein ERD4


Theoretical massNumber of molelcules
Total (without water)163,8972
Polymers163,8972
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein CSC1-like protein ERD4 / Hyperosmolality-gated Ca2+ permeable channel 3.1 / AtOSCA3.1 / Protein EARLY-RESPONSIVE TO ...Hyperosmolality-gated Ca2+ permeable channel 3.1 / AtOSCA3.1 / Protein EARLY-RESPONSIVE TO DEHYDRATION STRESS 4


Mass: 81948.672 Da / Num. of mol.: 2 / Mutation: Y367N/G454S/Y458I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ERD4, OSCA3.1, At1g30360, T4K22.4 / Production host: Homo sapiens (human) / References: UniProt: Q9C8G5

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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

ComponentName: Cryo-EM structure of OSCA3.1-1.1ver(Y367N-G454S-Y458I)-open/open state
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 49.41 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 116807 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00810950
ELECTRON MICROSCOPYf_angle_d0.85914946
ELECTRON MICROSCOPYf_dihedral_angle_d17.2491494
ELECTRON MICROSCOPYf_chiral_restr0.0491790
ELECTRON MICROSCOPYf_plane_restr0.0061832

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