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- EMDB-38612: Cryo-EM structure of OSCA3.1-1.1ver(Y367N-G454S-Y458I)-open/'dese... -

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Basic information

Entry
Database: EMDB / ID: EMD-38612
TitleCryo-EM structure of OSCA3.1-1.1ver(Y367N-G454S-Y458I)-open/'desensitized' state
Map data
Sample
  • Complex: Cryo-EM structure of OSCA3.1-1.1ver(Y367N-G454S-Y458I)-open/'desensitized' state
    • Protein or peptide: CSC1-like protein ERD4
KeywordsOSCA/TMEM63 channel / mechanosensitive channel / PLANT 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 thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsZhang Y / Han Y
Funding support China, Australia, 3 items
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, 2024-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38612.png

Downloads & links

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Map

FileDownload / File: emd_38612.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.055 Å
Density
Contour LevelBy AUTHOR: 0.264
Minimum - Maximum-1.4468169 - 2.3209283
Average (Standard dev.)0.0077181445 (±0.05651845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 253.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38612_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_38612_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 : Cryo-EM structure of OSCA3.1-1.1ver(Y367N-G454S-Y458I)-open/'dese...

EntireName: Cryo-EM structure of OSCA3.1-1.1ver(Y367N-G454S-Y458I)-open/'desensitized' state
Components
  • Complex: Cryo-EM structure of OSCA3.1-1.1ver(Y367N-G454S-Y458I)-open/'desensitized' state
    • Protein or peptide: CSC1-like protein ERD4

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Supramolecule #1: Cryo-EM structure of OSCA3.1-1.1ver(Y367N-G454S-Y458I)-open/'dese...

SupramoleculeName: Cryo-EM structure of OSCA3.1-1.1ver(Y367N-G454S-Y458I)-open/'desensitized' state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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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: 82.578344 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 NFFVAVTILF YMIPIAFVSA ITTLKNLQRI IPFI KPVVE ITAIRTVLES FLPQIALIVF LAMLPKLLLF LSKAEGIPSQ SHAIRAASSK YFIFSVFNVF 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 AGVSNSLEV

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

BufferpH: 7.9
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: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.41 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5z1f

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103405

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