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- EMDB-38730: Cryo-EM structure of TMEM63B-Digitonin state -

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Basic information

Entry
Database: EMDB / ID: EMD-38730
TitleCryo-EM structure of TMEM63B-Digitonin state
Map data
Sample
  • Complex: Cryo-EM structure of TMEM63B-Digitonin state
    • Protein or peptide: CSC1-like protein 2
KeywordsOSCA/TMEM63 channel / mechanosensitive channel / PLANT PROTEIN
Function / homology
Function and homology information


alveolar lamellar body membrane / sphingomyelin transfer activity / surfactant secretion / phosphatidylcholine transfer activity / mechanosensitive monoatomic cation channel activity / osmolarity-sensing monoatomic cation channel activity / intestinal stem cell homeostasis / phospholipid scramblase activity / drinking behavior / mechanosensitive monoatomic ion channel activity ...alveolar lamellar body membrane / sphingomyelin transfer activity / surfactant secretion / phosphatidylcholine transfer activity / mechanosensitive monoatomic cation channel activity / osmolarity-sensing monoatomic cation channel activity / intestinal stem cell homeostasis / phospholipid scramblase activity / drinking behavior / mechanosensitive monoatomic ion channel activity / calcium-activated cation channel activity / exocytosis / sensory perception of sound / actin cytoskeleton / early endosome membrane / lysosomal membrane / 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
Mechanosensitive cation channel TMEM63B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.84 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 15, 2024-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38730.png

Downloads & links

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Map

FileDownload / File: emd_38730.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 260 pix.
= 215.8 Å		0.83 Å/pix.
x 260 pix.
= 215.8 Å		0.83 Å/pix.
x 260 pix.
= 215.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.332
Minimum - Maximum-1.9977543 - 2.9842117
Average (Standard dev.)0.0027330054 (±0.06826993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 215.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38730_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38730_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of TMEM63B-Digitonin state

EntireName: Cryo-EM structure of TMEM63B-Digitonin state
Components
  • Complex: Cryo-EM structure of TMEM63B-Digitonin state
    • Protein or peptide: CSC1-like protein 2

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Supramolecule #1: Cryo-EM structure of TMEM63B-Digitonin state

SupramoleculeName: Cryo-EM structure of TMEM63B-Digitonin state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: CSC1-like protein 2

MacromoleculeName: CSC1-like protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.506609 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLPFLLATLG TTALNNSNPK DYCYSARIRS TVLQGLPFGG VPTVLALDFM CFLALLFLFS ILRKVAWDYG RLALVTDADR LRRQERDRV EQEYVASAMH GDSHDRYERL TSVSSSVDFD QRDNGFCSWL TAIFRIKDDE IRDKCGGDAV HYLSFQRHII G LLVVVGVL ...String:
MLPFLLATLG TTALNNSNPK DYCYSARIRS TVLQGLPFGG VPTVLALDFM CFLALLFLFS ILRKVAWDYG RLALVTDADR LRRQERDRV EQEYVASAMH GDSHDRYERL TSVSSSVDFD QRDNGFCSWL TAIFRIKDDE IRDKCGGDAV HYLSFQRHII G LLVVVGVL SVGIVLPVNF SGDLLENNAY SFGRTTIANL KSGNNLLWLH TSFAFLYLLL TVYSMRRHTS KMRYKEDDLV KR TLFINGI SKYAESEKIK KHFEEAYPNC TVLEARPCYN VARLMFLDAE RKKAERGKLY FTNLQSKENV PTMINPKPCG HLC CCVVRG CEQVEAIEYY TKLEQKLKED YKREKEKVNE KPLGMAFVTF HNETITAIIL KDFNVCKCQG CTCRGEPRPS SCSE SLHIS NWTVSYAPDP QNIYWEHLSI RGFIWWLRCL VINVVLFILL FFLTTPAIII TTMDKFNVTK PVEYLNNPII TQFFP TLLL WCFSALLPTI VYYSAFFEAH WTRSGENRTT MHKCYTFLIF MVLLLPSLGL SSLDLFFRWL FDKKFLAEAA IRFECV FLP DNGAFFVNYV IASAFIGNAM DLLRIPGLLM YMIRLCLARS AAERRNVKRH QAYEFQFGAA YAWMMCVFTV VMTYSIT CP IIVPFGLMYM LLKHLVDRYN LYYAYLPAKL DKKIHSGAVN QVVAAPILCL FWLLFFSTMR TGFLAPTSMF TFVVLVIT I VICLCHVCFG HFKYLSAHNY KIEHTETDTV DPRSNGRPPT AAAVPKSAKY IAQVLQDSEV DGDGDGAPGS SGDEPPSSS SQDEELLMPP DALTDTDFQS CEDSLIENEI HQSNSWSHPQ FEKL

UniProtKB: Mechanosensitive cation channel TMEM63B

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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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 63.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 378646
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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