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- EMDB-66358: Cryo-EM structure of TMEM63A-digitonin-cholesterol -

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Basic information

Entry
Database: EMDB / ID: EMD-66358
TitleCryo-EM structure of TMEM63A-digitonin-cholesterol
Map data
Sample
  • Complex: TMEM63A with cholesterol
    • Protein or peptide: Mechanosensitive cation channel TMEM63A
  • Ligand: CHOLESTEROL
Keywordsion channels / lipid scramblase / MEMBRANE PROTEIN
Function / homology
Function and homology information


surfactant secretion / osmolarity-sensing monoatomic cation channel activity / mechanosensitive monoatomic ion channel activity / calcium-activated cation channel activity / lysosome organization / tertiary granule membrane / specific granule membrane / centriolar satellite / early endosome membrane / nucleic acid binding ...surfactant secretion / osmolarity-sensing monoatomic cation channel activity / mechanosensitive monoatomic ion channel activity / calcium-activated cation channel activity / lysosome organization / tertiary granule membrane / specific granule membrane / centriolar satellite / early endosome membrane / nucleic acid binding / intracellular membrane-bounded organelle / lysosomal membrane / Neutrophil degranulation / extracellular exosome / 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 / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Mechanosensitive cation channel TMEM63A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsLin Y / Zhou Z / Han Y / Cheng D / Wang H / Ju L / Zhang Y / Cox DC / Corry B
Funding support Australia, China, 3 items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP200100860 Australia
Australian Research Council (ARC)FT220100159 Australia
Chinese Academy of Sciences2022ZD0207400 China
CitationJournal: Nat Commun / Year: 2026
Title: TMEM63 proteins act as mechanically activated cholesterol modulated lipid scramblases contributing to membrane mechano-resilience.
Authors: Yiechang Lin / Zijing Zhou / Yaoyao Han / Delfine Cheng / Haoqing Wang / Lining Arnold Ju / Yixiao Zhang / Charles D Cox / Ben Corry /
Abstract: OSCA/TMEM63 mechanosensitive ion channels play critical physiological roles in plants and animals. These channels bear structural homology to the dual functional TMEM16 family, and OSCA1.2 was ...OSCA/TMEM63 mechanosensitive ion channels play critical physiological roles in plants and animals. These channels bear structural homology to the dual functional TMEM16 family, and OSCA1.2 was recently shown to form a lipid-lined ion conduction pathway in the open state. This raised the question of whether members of the OSCA/TMEM63 family may also function as mechanically activated lipid scramblases. Using a combination of in vitro and cellular assays with computational techniques, we show that phospholipids can be translocated through the open pores of OSCA1.1/1.2/2.2 and TMEM63A/B proteins, suggesting a dual ion channel and lipid scramblase function for members of this protein family. We characterize the effects of mutating key groove lining residues demonstrating that different residues form bottlenecks for lipids and ions respectively and show that cholesterol inhibits lipid scrambling by stabilizing the closed state and slowing translocation through the open pore. We show that lipid scrambling in TMEM63 proteins can be activated by mechanical forces in the membrane, making these mechanically activated lipid scramblases. Finally, we demonstrate that this activity is important for the mechanically induced morphological remodeling of biological membranes and the resilience of cells to high mechanical forces.
History
DepositionSep 26, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_66358.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.495
Minimum - Maximum-1.9465182 - 2.628644
Average (Standard dev.)0.00576299 (±0.06529964)
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_66358_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_66358_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : TMEM63A with cholesterol

EntireName: TMEM63A with cholesterol
Components
  • Complex: TMEM63A with cholesterol
    • Protein or peptide: Mechanosensitive cation channel TMEM63A
  • Ligand: CHOLESTEROL

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Supramolecule #1: TMEM63A with cholesterol

SupramoleculeName: TMEM63A with cholesterol / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Mechanosensitive cation channel TMEM63A

MacromoleculeName: Mechanosensitive cation channel TMEM63A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 92.743367 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MMDSPFLELW QSKAVSIREQ LGLGDRPNDS YCYNSAKNST VLQGVTFGGI PTVLLIDVSC FLFLILVFSI IRRRFWDYGR IALVSEADS ESRFQRLSST SSSGQQDFEN ELGCCPWLTA IFRLHDDQIL EWCGEDAIHY LSFQRHIIFL LVVVSFLSLC V ILPVNLSG ...String:
MMDSPFLELW QSKAVSIREQ LGLGDRPNDS YCYNSAKNST VLQGVTFGGI PTVLLIDVSC FLFLILVFSI IRRRFWDYGR IALVSEADS ESRFQRLSST SSSGQQDFEN ELGCCPWLTA IFRLHDDQIL EWCGEDAIHY LSFQRHIIFL LVVVSFLSLC V ILPVNLSG DLLDKDPYSF GRTTIANLQT DNDLLWLHTI FAVIYLFLTV GFMRHHTQSI KYKEENLVRR TLFITGLPRD AR KETVESH FRDAYPTCEV VDVQLCYNVA KLIYLCKEKK KTEKSLTYYT NLQVKTGQRT LINPKPCGQF CCCEVLGCEW EDA ISYYTR MKDRLLERIT EEERHVQDQP LGMAFVTFQE KSMATYILKD FNACKCQSLQ CKGEPQPSSH SRELYTSKWT VTFA ADPED ICWKNLSIQG LRWWLQWLGI NFTLFLGLFF LTTPSIILST MDKFNVTKPI HALNNPIISQ FFPTLLLWSF SALLP SIVY YSTLLESHWT KSGENQIMMT KVYIFLIFMV LILPSLGLTS LDFFFRWLFD KTSSEASIRL ECVFLPDQGA FFVNYV IAS AFIGNGMELL RLPGLILYTF RMIMAKTAAD RRNVKQNQAF QYEFGAMYAW MLCVFTVIVA YSITCPIIAP FGLIYIL LK HMVDRHNLYF VYLPAKLEKG IHFAAVNQAL AAPILCLFWL YFFSFLRLGM KAPATLFTFL VLLLTILVCL AHTCFGCF K HLSPLNYKTE EPASDKGSEA EAHMPPPFTP YVPRILNGLA SERTALSPQQ QQQQTYGAIH NISGTIPGQC LAQSATGSV AAAPQEASNS LE

UniProtKB: Mechanosensitive cation channel TMEM63A

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Macromolecule #2: CHOLESTEROL

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

ChemComp-CLR:
CHOLESTEROL

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 63.9 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: PDB ENTRY
PDB model - PDB ID:
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 202829
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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