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- PDB-9o1q: TMEM16F D409G mutant in liposomes in the presence of Ca2+ (active... -

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Basic information

Entry
Database: PDB / ID: 9o1q
TitleTMEM16F D409G mutant in liposomes in the presence of Ca2+ (active state)
ComponentsAnoctamin-6
KeywordsLIPID TRANSPORT / membrane protein / lipid scramblase / TMEM16 / liposome
Function / homology
Function and homology information


calcium activated galactosylceramide scrambling / phosphatidylserine exposure on blood platelet / calcium activated phosphatidylserine scrambling / calcium activated phosphatidylcholine scrambling / calcium activated phospholipid scrambling / positive regulation of potassium ion export across plasma membrane / positive regulation of monoatomic ion transmembrane transport / activation of blood coagulation via clotting cascade / purinergic nucleotide receptor signaling pathway / phospholipid scramblase activity ...calcium activated galactosylceramide scrambling / phosphatidylserine exposure on blood platelet / calcium activated phosphatidylserine scrambling / calcium activated phosphatidylcholine scrambling / calcium activated phospholipid scrambling / positive regulation of potassium ion export across plasma membrane / positive regulation of monoatomic ion transmembrane transport / activation of blood coagulation via clotting cascade / purinergic nucleotide receptor signaling pathway / phospholipid scramblase activity / bone mineralization involved in bone maturation / cholinergic synapse / intracellularly calcium-gated chloride channel activity / pore complex assembly / negative regulation of cell volume / plasma membrane phospholipid scrambling / voltage-gated monoatomic ion channel activity / bleb assembly / positive regulation of phagocytosis, engulfment / Stimuli-sensing channels / voltage-gated chloride channel activity / calcium-activated cation channel activity / positive regulation of monocyte chemotaxis / dendritic cell chemotaxis / chloride transport / phospholipid translocation / chloride channel activity / regulation of postsynaptic membrane potential / positive regulation of endothelial cell apoptotic process / positive regulation of bone mineralization / chloride channel complex / Neutrophil degranulation / chloride transmembrane transport / sodium ion transmembrane transport / synaptic membrane / calcium ion transmembrane transport / blood coagulation / positive regulation of apoptotic process / protein homodimerization activity / metal ion binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Anoctamin, dimerisation domain / Anoctamin, dimerisation domain / Anoctamin / : / Calcium-activated chloride channel
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsFeng, Z. / Accardi, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM152012 United States
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: Calcium dependent activation of the TMEM16F scramblase and ion channel.
Authors: Zhang Feng / Omar E Alvarenga / Eleonora Di Zanni / Sangyun Lee / George Khelashvili / Alessio Accardi /
Abstract: The ubiquitous transmembrane protein 16F (TMEM16F) Ca-activated channel and scramblase catalyzes phosphatidylserine externalization to enable blood coagulation, membrane fusion and brain immune ...The ubiquitous transmembrane protein 16F (TMEM16F) Ca-activated channel and scramblase catalyzes phosphatidylserine externalization to enable blood coagulation, membrane fusion and brain immune surveillance. Despite its importance, the molecular mechanisms underlying TMEM16F activation remain poorly understood. Here, we obtained high-resolution cryo-electron microscopy structures of TMEM16F active in liposomes. In high-activity conditions, TMEM16F adopts two conformations, the canonical Ca-bound closed state and one where the upward rotation of the cytosolic domain leads to an X-shaped groove that forms a transmembrane pore and locally thins the membrane. Using mutagenesis, functional assays and molecular dynamics simulations, we show that the X-shaped groove is active and mediates nonselective ion flux and lipid scrambling through distinct pathways; ions move within the protein-delimited pore, whereas lipids skirt the X-shaped groove. Our findings provide a complete picture of TMEM16F Ca-dependent gating and demonstrate that imaging membrane proteins in a native-like environment can allow capturing otherwise inaccessible active states.
History
DepositionApr 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
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Revision 1.0May 6, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anoctamin-6
B: Anoctamin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,8608
Polymers212,6192
Non-polymers2406
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 Anoctamin-6 / Small-conductance calcium-activated nonselective cation channel / SCAN channel / Transmembrane ...Small-conductance calcium-activated nonselective cation channel / SCAN channel / Transmembrane protein 16F / TMEM16F


Mass: 106309.688 Da / Num. of mol.: 2 / Mutation: D409G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ano6, Tmem16f / Production host: Homo sapiens (human) / References: UniProt: Q6P9J9
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: Dimeric lipid scramblase and ion channel mTMEM16F / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.21 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTris1
2150 mMpotassium chlorideKCl1
31 mMcalcium chlorideCaCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50.02 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4330881
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143932 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingPDB-ID: 6QP6

6qp6


Accession code: 6QP6 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312634
ELECTRON MICROSCOPYf_angle_d0.61817140
ELECTRON MICROSCOPYf_dihedral_angle_d3.9951656
ELECTRON MICROSCOPYf_chiral_restr0.0411876
ELECTRON MICROSCOPYf_plane_restr0.0052142

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