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- EMDB-38456: Cryo-EM structure of Ca2+-bound TMEM16A in complex with Tamsulosin -

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Basic information

Entry
Database: EMDB / ID: EMD-38456
TitleCryo-EM structure of Ca2+-bound TMEM16A in complex with Tamsulosin
Map data
Sample
  • Complex: Structure of Tamsulosin- and calcium-bound mTMEM16A chloride channel
    • Protein or peptide: Anoctamin-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: TETRADECANE
  • Ligand: CALCIUM ION
  • Ligand: Tamsulosin
  • Ligand: HEXANE
KeywordsInhibitor / Modulator / Complex / Ion channel / LIPID BINDING PROTEIN
Function / homology
Function and homology information


glial cell projection elongation / trachea development / mucus secretion / intracellularly calcium-gated chloride channel activity / voltage-gated chloride channel activity / Stimuli-sensing channels / chloride transport / chloride channel activity / detection of temperature stimulus involved in sensory perception of pain / positive regulation of insulin secretion involved in cellular response to glucose stimulus ...glial cell projection elongation / trachea development / mucus secretion / intracellularly calcium-gated chloride channel activity / voltage-gated chloride channel activity / Stimuli-sensing channels / chloride transport / chloride channel activity / detection of temperature stimulus involved in sensory perception of pain / positive regulation of insulin secretion involved in cellular response to glucose stimulus / chloride channel complex / chloride transmembrane transport / regulation of membrane potential / cell projection / establishment of localization in cell / presynaptic membrane / cellular response to heat / phospholipase C-activating G protein-coupled receptor signaling pathway / apical plasma membrane / external side of plasma membrane / glutamatergic synapse / protein homodimerization activity / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Anoctamin, dimerisation domain / Anoctamin, dimerisation domain / Anoctamin / : / Calcium-activated chloride channel
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / Resolution: 2.93 Å
AuthorsLi HL / Li SL / Li S
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Tamsulosin ameliorates bone loss by inhibiting the release of Cl through wedging into an allosteric site of TMEM16A.
Authors: Shiliang Li / Weijia Sun / Shuang Li / Lili Zhu / Shuai Guo / Jiaqi He / Yuheng Li / Chaoquan Tian / Zhenjiang Zhao / Tao Yu / Jianwei Li / Yiqing Zhang / Youlong Hai / Jiawen Wang / Yongjun ...Authors: Shiliang Li / Weijia Sun / Shuang Li / Lili Zhu / Shuai Guo / Jiaqi He / Yuheng Li / Chaoquan Tian / Zhenjiang Zhao / Tao Yu / Jianwei Li / Yiqing Zhang / Youlong Hai / Jiawen Wang / Yongjun Zheng / Rui Wang / Xiaoyong Hu / Shukuan Ling / Honglin Li / Yingxian Li /
Abstract: TMEM16A, a key calcium-activated chloride channel, is crucial for many physiological and pathological processes such as cancer, hypertension, and osteoporosis, etc. However, the regulatory mechanism ...TMEM16A, a key calcium-activated chloride channel, is crucial for many physiological and pathological processes such as cancer, hypertension, and osteoporosis, etc. However, the regulatory mechanism of TMEM16A is poorly understood, limiting the discovery of effective modulators. Here, we unveil an allosteric gating mechanism by presenting a high-resolution cryo-EM structure of TMEM16A in complex with a channel inhibitor that we identified, Tamsulosin, which is resolved at 2.93 Å. Tamsulosin wedges itself into a pocket within the extracellular domain of TMEM16A, surrounded by α1-α2, α5-α6, and α9-α10 loops. This binding stabilizes a transient preopen conformation of TMEM16A, which is activated by Ca ions while still preserving a closed pore to prevent Cl permeation. Validation of this binding site through computational, electrophysiological, and functional experiments, along with site-directed mutagenesis, confirmed the pivotal roles of the pocket-lining residues R605 and E624 on α5-α6 loop in modulating Tamsulosin binding and pore activity. Tamsulosin induces significant positional shifts in extracellular loops, particularly the α5-α6 loop, which moves toward the extracellular exit of the pore, leading to noticeable structural rearrangements in pore-lining helices. The hinges induced by P595 in α5 and G711 in α7 introduce flexibility to the transmembrane helices, orienting Y593 to collaborate with I641 in effectively gating the preopening pore. Notably, Tamsulosin demonstrates significant antiosteoporotic effects by inhibiting TMEM16A, suggesting potential for its repurposing in new therapeutic indications. Our study not only enhances our understanding of the gating mechanism of TMEM16A inhibition but also facilitates structure-based drug design targeting TMEM16A.
History
DepositionDec 26, 2023-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38456.png

Downloads & links

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Map

FileDownload / File: emd_38456.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 384 pix.
= 330.24 Å		0.86 Å/pix.
x 384 pix.
= 330.24 Å		0.86 Å/pix.
x 384 pix.
= 330.24 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.65
Minimum - Maximum-8.2637415 - 10.293952000000001
Average (Standard dev.)0.0024302977 (±0.16029274)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 330.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38456_half_map_1.map
Projections & Slices
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Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_38456_half_map_2.map
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Sample components

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Entire : Structure of Tamsulosin- and calcium-bound mTMEM16A chloride channel

EntireName: Structure of Tamsulosin- and calcium-bound mTMEM16A chloride channel
Components
  • Complex: Structure of Tamsulosin- and calcium-bound mTMEM16A chloride channel
    • Protein or peptide: Anoctamin-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: TETRADECANE
  • Ligand: CALCIUM ION
  • Ligand: Tamsulosin
  • Ligand: HEXANE

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Supramolecule #1: Structure of Tamsulosin- and calcium-bound mTMEM16A chloride channel

SupramoleculeName: Structure of Tamsulosin- and calcium-bound mTMEM16A chloride channel
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Anoctamin-1

MacromoleculeName: Anoctamin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 111.058992 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRVPEKYSTL PAEDRSVHIV NICAIEDLGY LPSEGTLLNS LSVDPDAECK YGLYFRDGKR KVDYILVYHH KRASGSRTLA RRGLQNDMV LGTRSVRQDQ PLPGKGSPVD AGSPEVPMDY HEDDKRFRRE EYEGNLLEAG LELENDEDTK IHGVGFVKIH A PWHVLCRE ...String:
MRVPEKYSTL PAEDRSVHIV NICAIEDLGY LPSEGTLLNS LSVDPDAECK YGLYFRDGKR KVDYILVYHH KRASGSRTLA RRGLQNDMV LGTRSVRQDQ PLPGKGSPVD AGSPEVPMDY HEDDKRFRRE EYEGNLLEAG LELENDEDTK IHGVGFVKIH A PWHVLCRE AEFLKLKMPT KKVYHISETR GLLKTINSVL QKITDPIQPK VAEHRPQTTK RLSYPFSREK QHLFDLTDRD SF FDSKTRS TIVYEILKRT TCTKAKYSMG ITSLLANGVY SAAYPLHDGD YEGDNVEFND RKLLYEEWAS YGVFYKYQPI DLV RKYFGE KVGLYFAWLG AYTQMLIPAS IVGVIVFLYG CATVDENIPS MEMCDQRYNI TMCPLCDKTC SYWKMSSACA TARA SHLFD NPATVFFSVF MALWAATFME HWKRKQMRLN YRWDLTGFEE EEEAVKDHPR AEYEARVLEK SLRKESRNKE TDKVK LTWR DRFPAYFTNL VSIIFMIAVT FAIVLGVIIY RISTAAALAM NSSPSVRSNI RVTVTATAVI INLVVIILLD EVYGCI ARW LTKIEVPKTE KSFEERLTFK AFLLKFVNSY TPIFYVAFFK GRFVGRPGDY VYIFRSFRME ECAPGGCLME LCIQLSI IM LGKQLIQNNL FEIGIPKMKK FIRYLKLRRQ SPSDREEYVK RKQRYEVDFN LEPFAGLTPE YMEMIIQFGF VTLFVASF P LAPLFALLNN IIEIRLDAKK FVTELRRPVA IRAKDIGIWY NILRGVGKLA VIINAFVISF TSDFIPRLVY LYMYSQNGT MHGFVNHTLS SFNVSDFQNG TAPNDPLDLG YEVQICRYKD YREPPWSEHK YDISKDFWAV LAARLAFVIV FQNLVMFMSD FVDWVIPDI PKDISQQIHK EKVLMVELFM REEQGKQQLL DTWMEKEKPR DVPCNNHSPT THPEAGDGSP VPSYEYHGDA L

UniProtKB: Anoctamin-1

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #3: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 3 / Number of copies: 50 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: Tamsulosin

MacromoleculeName: Tamsulosin / type: ligand / ID: 5 / Number of copies: 2 / Formula: JGX
Molecular weightTheoretical: 408.512 Da
Chemical component information

ChemComp-JGX:
Tamsulosin

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Macromolecule #6: HEXANE

MacromoleculeName: HEXANE / type: ligand / ID: 6 / Number of copies: 2 / Formula: HEX
Molecular weightTheoretical: 86.175 Da
Chemical component information

ChemComp-HEX:
HEXANE

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMNaClsodium chloride
0.5 mMCaCl2calcium chloride
GridModel: Quantifoil R1.2/1.3 / Mesh: 300

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12322
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8xlr:
Cryo-EM structure of Ca2+-bound TMEM16A in complex with Tamsulosin

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