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Yorodumi- EMDB-3861: Cryo-EM map of calcium-free mTMEM16A chloride channel at 4.06 A r... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3861 | |||||||||
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Title | Cryo-EM map of calcium-free mTMEM16A chloride channel at 4.06 A resolution | |||||||||
Map data | None | |||||||||
Sample |
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Function / homology | Function and homology information glial cell projection elongation / trachea development / iodide transmembrane transporter activity / iodide transport / intracellularly calcium-gated chloride channel activity / mucus secretion / cellular response to peptide / voltage-gated chloride channel activity / Stimuli-sensing channels / chloride transport ...glial cell projection elongation / trachea development / iodide transmembrane transporter activity / iodide transport / intracellularly calcium-gated chloride channel activity / mucus secretion / cellular response to peptide / voltage-gated chloride channel activity / Stimuli-sensing channels / chloride transport / chloride channel activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / detection of temperature stimulus involved in sensory perception of pain / chloride channel complex / chloride transmembrane transport / regulation of membrane potential / establishment of localization in cell / cell projection / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / cellular response to heat / apical plasma membrane / external side of plasma membrane / signaling receptor binding / glutamatergic synapse / protein homodimerization activity / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.06 Å | |||||||||
Authors | Paulino C / Kalienkova V / Lam KM / Neldner Y / Dutzler R | |||||||||
Funding support | Switzerland, 2 items
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Citation | Journal: Nature / Year: 2017 Title: Activation mechanism of the calcium-activated chloride channel TMEM16A revealed by cryo-EM. Authors: Cristina Paulino / Valeria Kalienkova / Andy K M Lam / Yvonne Neldner / Raimund Dutzler / Abstract: The calcium-activated chloride channel TMEM16A is a ligand-gated anion channel that opens in response to an increase in intracellular Ca concentration. The protein is broadly expressed and ...The calcium-activated chloride channel TMEM16A is a ligand-gated anion channel that opens in response to an increase in intracellular Ca concentration. The protein is broadly expressed and contributes to diverse physiological processes, including transepithelial chloride transport and the control of electrical signalling in smooth muscles and certain neurons. As a member of the TMEM16 (or anoctamin) family of membrane proteins, TMEM16A is closely related to paralogues that function as scramblases, which facilitate the bidirectional movement of lipids across membranes. The unusual functional diversity of the TMEM16 family and the relationship between two seemingly incompatible transport mechanisms has been the focus of recent investigations. Previous breakthroughs were obtained from the X-ray structure of the lipid scramblase of the fungus Nectria haematococca (nhTMEM16), and from the cryo-electron microscopy structure of mouse TMEM16A at 6.6 Å (ref. 14). Although the latter structure disclosed the architectural differences that distinguish ion channels from lipid scramblases, its low resolution did not permit a detailed molecular description of the protein or provide any insight into its activation by Ca. Here we describe the structures of mouse TMEM16A at high resolution in the presence and absence of Ca. These structures reveal the differences between ligand-bound and ligand-free states of a calcium-activated chloride channel, and when combined with functional experiments suggest a mechanism for gating. During activation, the binding of Ca to a site located within the transmembrane domain, in the vicinity of the pore, alters the electrostatic properties of the ion conduction path and triggers a conformational rearrangement of an α-helix that comes into physical contact with the bound ligand, and thereby directly couples ligand binding and pore opening. Our study describes a process that is unique among channel proteins, but one that is presumably general for both functional branches of the TMEM16 family. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3861.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-3861-v30.xml emd-3861.xml | 24.7 KB 24.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3861_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_3861.png | 1.1 MB | ||
Masks | emd_3861_msk_1.map | 64 MB | Mask map | |
Others | emd_3861_additional.map.gz emd_3861_half_map_1.map.gz emd_3861_half_map_2.map.gz | 59.9 MB 56.4 MB 56.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3861 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3861 | HTTPS FTP |
-Validation report
Summary document | emd_3861_validation.pdf.gz | 448.7 KB | Display | EMDB validaton report |
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Full document | emd_3861_full_validation.pdf.gz | 447.8 KB | Display | |
Data in XML | emd_3861_validation.xml.gz | 14.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3861 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3861 | HTTPS FTP |
-Related structure data
Related structure data | 5oygMC 3860C 5oybC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3861.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.365 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_3861_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: None
File | emd_3861_additional.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryo-EM half map 2 of the ion channel...
File | emd_3861_half_map_1.map | ||||||||||||
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Annotation | cryo-EM half map 2 of the ion channel TMEM16A from mouse in absence of calcium ions | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryo-EM half map 1 of the ion channel...
File | emd_3861_half_map_2.map | ||||||||||||
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Annotation | cryo-EM half map 1 of the ion channel TMEM16A from mouse in absence of calcium ions | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : mTMEM16A in absence of calcium ions
Entire | Name: mTMEM16A in absence of calcium ions |
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Components |
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-Supramolecule #1: mTMEM16A in absence of calcium ions
Supramolecule | Name: mTMEM16A in absence of calcium ions / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: calcium-activated chloride channel |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: HEK293 / Recombinant cell: stabel mTMEM16A cell line (Flp-In System) |
Molecular weight | Experimental: 110.916 KDa |
-Macromolecule #1: Anoctamin-1
Macromolecule | Name: Anoctamin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 111.058992 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.3 mg/mL |
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Buffer | pH: 7.5 / Component - Concentration: 20.0 mM / Component - Name: Hepes / Details: 20 mM Hepes 150 mM NaCl <0.12% digitonin |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV / Details: 2 ul sample volume 2-4 sec blotting time. |
Details | full-length (wild-type isoform ac) deglycosylated mTMEM16A in absence of CaCl2 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80.0 K / Max: 100.0 K |
Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV / Energy filter - Lower energy threshold: -10 eV / Energy filter - Upper energy threshold: +10 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7420 pixel / Digitization - Dimensions - Height: 7676 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-100 / Number grids imaged: 3 / Number real images: 5063 / Average exposure time: 15.0 sec. / Average electron dose: 80.0 e/Å2 Details: Data were collected in an automated fashion using SerialEM47 on a K2 Summit detector (Gatan). The dataset in absence of calcium ions was obtained at a pixel size of 0.6825A in super- ...Details: Data were collected in an automated fashion using SerialEM47 on a K2 Summit detector (Gatan). The dataset in absence of calcium ions was obtained at a pixel size of 0.6825A in super-resolution mode, a defocus range of -0.5 to -3.9 um, an exposure time of 15 sec and a sub-frame exposure time of 150 ms (100 frames) with an electron dose at the specimen level of 0.75-0.8 e-/A2/frame. The total accumulated dose on the specimen level was approximately 80 e-/A2. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.8 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 36630 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.8 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 36630 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-5oyg: |