1. Biochemistry and Chemical Biology
  2. Structural Biology and Molecular Biophysics
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Stepwise activation mechanism of the scramblase nhTMEM16 revealed by cryo-EM

  1. Valeria Kalienkova
  2. Vanessa Clerico Mosina
  3. Laura Bryner
  4. Gert T Oostergetel
  5. Raimund Dutzler  Is a corresponding author
  6. Cristina Paulino  Is a corresponding author
  1. University of Zurich, Switzerland
  2. University of Groningen, The Netherlands
Research Article
Cite this article as: eLife 2019;8:e44364 doi: 10.7554/eLife.44364
8 figures, 2 videos, 3 tables, 12 data sets and 1 additional file

Figures

Figure 1 with 5 supplements
Cryo-EM structures of nhTMEM16 in detergent.

Ribbon representation of the Ca2+-bound cryo-EM structure of nhTMEM16 in detergent. The view is from within the membrane perpendicular to the long dimension of the protein (A), towards the subunit cavity (B) and at the Ca2+-ion binding site (C). The membrane boundary is indicated. Subunits in the dimer are depicted in orange and gray, respective transmembrane-helices are labelled and Ca2+-ions are displayed as blue spheres. Relative orientations are indicated and the location of the Ca2+-binding site is highlighted by a box in panel B. (D) Cryo-EM map of the nhTMEM16 dimer (orange and gray) in DDM in presence of Ca2+ at 3.6 Å, sharpened with a b-factor of –126 Å2 and contoured at 6 σ. (E) Ribbon representation of a superposition of the Ca2+-bound structure in detergent determined by cryo-EM (orange and gray) and the Ca2+-bound X-ray structure (dark gray and light blue, PDBID: 4WIS) The view is as in panel B. (F) View of the Ca2+-ion binding site of the Ca2+-bound state of nhTMEM16 in DDM. Ca2+-ions are displayed as blue spheres. (G) Cryo-EM map of the nhTMEM16 dimer (green and gray) in DDM in the absence of Ca2+ at 3.7 Å, sharpened with a b-factor of –147 Å2 and contoured at 6 σ. (H) Ribbon representation of a superposition of the Ca2+-bound (orange and gray) and the Ca2+-free structure (green and gray) in detergent determined by cryo-EM. The view is as in panel B. (I) View of the Ca2+-binding site in the Ca2+-free state of nhTMEM16 in DDM. The location of weak residual density at the center of the Ca2+-binding site is indicated in magenta. F,I The respective cryo-EM densities are contoured at 7 σ and shown as mesh. The backbone is displayed as Cα-trace, selected side-chains as sticks.

https://doi.org/10.7554/eLife.44364.002
Figure 1—figure supplement 1
Reconstitution of nhTMEM16 into liposomes.

Ca2+-dependence of scrambling activity of WT in liposomes of three different lipid compositions. Traces depict the fluorescence decrease of tail-labeled NBD-PE lipids after addition of dithionite (#) at different Ca2+ concentrations. Data show averages of three technical replicates for assay and nanodisc lipids, and of two for soybean lipids. Ca2+ concentrations (μM) are indicated. (A) Scrambling activity of nhTMEM16 reconstituted into liposomes composed of E. coli polar lipids, egg PC at a ratio of 3:1 (w/w) used for functional experiments. (B) Scrambling activity of nhTMEM16 reconstituted into liposomes composed of soybean polar lipids extract with 20% cholesterol (mol/mol). (C) Scrambling activity of nhTMEM16 reconstituted into liposomes composed of POPC/POPG at a molar ratio of 7:3 used for nanodisc assembly. Traces of E. coli polar lipids/egg PC-containing proteoliposomes (displayed in A) are shown as dashed lines for comparison.

https://doi.org/10.7554/eLife.44364.003
Figure 1—figure supplement 2
Structure Determination of nhTMEM16 in DDM in complex with Ca2+.

(A) Representative cryo-EM image and (B) 2D-class averages of vitrified nhTMEM16 in a Ca2+-bound state in detergent. (C) Angular distribution plot of particles included in the final C2-symmetric 3D reconstruction. The number of particles with their respective orientation is represented by length and color of the cylinders. (D) Image processing workflow. (E) FSC plot used for resolution estimation and model validation. The gold-standard FSC plot between two separately refined half-maps is shown in orange and indicates a final resolution of 3.6 Å. FSC validation curves for FSCsum, FSCwork and FSCfree as described in the Methods are shown in light yellow, dark gray and light gray, respectively. A thumbnail of the mask used for FSC calculation overlaid on the atomic model is shown in the upper right corner and thresholds used for FSCsum of 0.5 and for FSC of 0.143 are shown as dashed lines. (F) Anisotropy estimation plot of the final map. The global FSC curve is represented in yellow. The directional FSCs along the x, y and z axis displayed in blue, green and red, respectively, are indicative for an isotropic dataset. (G) Final reconstruction map colored by local resolution as estimated by Relion, indicate regions of higher resolution. (H) Sections of the cryo-EM density of the map superimposed on the refined model. The model is shown as sticks and structural elements are labelled. The map was sharpened with a b-factor of –126 Å2 and contoured at 5 σ.

https://doi.org/10.7554/eLife.44364.004
Figure 1—figure supplement 3
Structure Determination of nhTMEM16 in DDM in absence of Ca2+.

(A) Representative cryo-EM image and (B) 2D-class averages of vitrified nhTMEM16 in a Ca2+-free state in detergent. (C) Angular distribution plot of particles included in the final C2-symmetric 3D reconstruction. The number of particles with their respective orientation is represented by length and color of the cylinders. (D) Image processing workflow. (E) FSC plot used for resolution estimation and model validation. The gold-standard FSC plot between two separately refined half-maps is shown in green and indicates a final resolution of 3.7 Å. FSC validation curves for FSCsum, FSCwork and FSCfree as described in the Methods are shown in cyan, dark gray and light gray, respectively. A thumbnail of the mask used for FSC calculation overlaid on the atomic model is shown in the upper right corner and thresholds used for FSCsum of 0.5 and for FSC of 0.143 are shown as dashed lines. (F) Anisotropy estimation plot of the final map. The global FSC curve is represented in yellow. The directional FSCs along the x, y and z axis displayed in blue, green and red, respectively, are indicative for an isotropic dataset. (G) Final reconstruction map colored by local resolution as estimated by Relion, indicate regions of higher resolution. (H) Sections of the cryo-EM density of the map superimposed on the refined model. The model is shown as sticks and structural elements are labelled. The map was sharpened with a b-factor of –147 Å2 and contoured at 5 σ.

https://doi.org/10.7554/eLife.44364.005
Figure 1—figure supplement 4
Sequence alignment of selected TMEM16 scramblases.

Protein sequences of the transmembrane domain of the fungal TMEM16 homologs from Nectria haematococca (nhTMEM16) and Aspergillus fumigatus (afTMEM16), murine TMEM16F and human TMEM16K were aligned based on their structure. Numbering and the boundaries of secondary structure elements (green rectangles for transmembrane-helices and green lines for loops) correspond to nhTMEM16. Residues highlighted in red constitute the Ca2+-binding site; residues highlighted in blue act as potential pivot points for structural rearrangements in α4; residue highlighted in purple indicates the flexible hinge region in TMEM16F responsible for the movements of α6 upon Ca2+ release.

https://doi.org/10.7554/eLife.44364.006
Figure 1—figure supplement 5
Detergent binding to the subunit cavity.

(A) Cryo-EM map of the nhTMEM16 dimer in detergents in presence of Ca2+ (gray) in two orientations. Residual density in the subunit cavity highlighted in orange. (B) Ribbon representation of the subunit cavity of nhTMEM16 in detergent in presence of Ca2+. Residual density (contoured at 5 σ) is shown as gray mesh. A DDM molecule (yellow) and selected sidechains are depicted as sticks. (C) Cryo-EM map of the nhTMEM16 dimer in detergent in absence of Ca2+ (gray) in two orientations. Residual density found in the subunit cavity is highlighted in green. (D) Ribbon representation of the subunit cavity of nhTMEM16 in detergents in absence of Ca2+ (green). Residual density (contoured at 5 σ) is shown as gray mesh. A DDM molecule (yellow) and selected sidechains are depicted as sticks. The location of B,D is indicated by the box drawn on the right panel of A,C.

https://doi.org/10.7554/eLife.44364.007
Figure 2 with 2 supplements
Cryo-EM structure of nhTMEM16 in nanodiscs in absence of Ca2+.

(A) Cryo-EM map of the nhTMEM16 dimer (light green and gray) in nanodiscs in absence of Ca2+ at 3.8 Å resolution. The map was sharpened with a b-factor of –150 Å2 and is contoured at 5.6 σ. (B) View of the Ca2+-binding site in the Ca2+-free state of nhTMEM16 in nanodiscs. The cryo-EM density shown as mesh is contoured at 6 σ, the backbone is displayed as Cα-trace and selected side-chains as sticks. (C) Cα-traces of α6 from a superposition of Ca2+-free structures of nhTMEM16 in nanodiscs (green), TMEM16A (violet, PDBID: 5OYG) and TMEM16F (red, PDBID: 6QPB) and of the Ca2+-bound structure of nhTMEM16 in DDM (gray). The spheres indicate the position of the flexible glycine residue in TMEM16A and TMEM16F, which acts as a hinge for conformational changes. (D–F) Ribbon representation of superpositions of the Ca2+-free structure in nanodiscs (light green and gray) with the Ca2+-bound structure in DDM ((D), orange and gray), the Ca2+-free structure of TMEM16A ((E), violet, PDBID: 5OYG) and the Ca2+-free structure of TMEM16F ((F), red, PDBID: 6QPB). Selected α-helices are labeled, the views are as in Figure 1.

https://doi.org/10.7554/eLife.44364.009
Figure 2—figure supplement 1
Reconstitution of nhTMEM16 into nanodiscs.

Shape of nhTMEM16 particles reconstituted into nanodiscs at different protein to lipid ratios (LPR, mol/mol) in the absence of Ca2+: (A), LPR 145, (B), LPR 155 and (C), LPR 220. Refined and unmasked cryo-EM density maps were low-pass filtered to 10 Å and are shown from the extracellular side (upper panel, subunit cavity indicated by *) and from the side with a view towards the subunit cavity (lower panel). A model of nhTMEM16 fitted into the density is displayed as ribbon.

https://doi.org/10.7554/eLife.44364.010
Figure 2—figure supplement 2
Structure Determination of nhTMEM16 in the absence of Ca2+ in nanodiscs.

(A) Representative cryo-EM image and (B) 2D-class averages of vitrified nhTMEM16 in a Ca2+-free state in lipid nanodiscs. (C) Angular distribution plot of particles included in the final C2-symmetric 3D reconstruction. The number of particles with their respective orientation is represented by length and color of the cylinders. (D) Image processing workflow. (E) FSC plot used for resolution estimation and model validation. The gold-standard FSC plot between two separately refined half-maps is shown in green and indicates a final resolution of 3.8 Å. FSC validation curves for FSCsum, FSCwork and FSCfree as described in the Methods are shown in light green, dark gray and light gray, respectively. A thumbnail of the mask used for FSC calculation overlaid on the atomic model is shown in the upper right corner and thresholds used for FSCsum of 0.5 and for FSC of 0.143 are shown as dashed lines. (F) Anisotropy estimation plot of the final map. The global FSC curve is represented in yellow. The directional FSCs along the x, y and z axis displayed in blue, green and red, respectively, are indicative for an isotropic dataset. (G) Final reconstruction map colored by local resolution as estimated by Relion, indicate regions of higher resolution. (H) Sections of the cryo-EM density of the map superimposed on the refined model. The model is shown as sticks and structural elements are labelled. The map was sharpened with a b-factor of –150 Å2 and contoured at 5 σ.

https://doi.org/10.7554/eLife.44364.011
Figure 3 with 3 supplements
Cryo-EM structures of nhTMEM16 in nanodiscs in presence of Ca2+.

(A) Cryo-EM map of the nhTMEM16 dimer in the Ca2+-bound ‘open’ state (yellow and gray) in nanodiscs at 3.6 Å, sharpened with a b-factor of –114 Å2 and contoured at 6.5 σ (upper panel). Close-up of the Ca2+-binding site with two bound Ca2+-ions displayed as blue spheres (lower panel). Cryo-EM density contoured at 7 σ is shown as gray mesh, the backbone is displayed as yellow Cα-trace and selected side-chains as sticks. (B) Cryo-EM map of the nhTMEM16 dimer in the Ca2+-bound ‘intermediate’ state (yellow-green and gray) in nanodiscs at 3.7 Å, sharpened with a b-factor of –96 Å2 and contoured at 4.9 σ (upper panel). Close-up of the Ca2+-binding site with two bound Ca2+-ions displayed as blue spheres (lower panel). Cryo-EM density contoured at 7 σ is shown as gray mesh, the backbone is displayed as light green Cα-trace and selected side-chains as sticks. (C) Cryo-EM map of the nhTMEM16 dimer in the ‘Ca2+-bound closed state (green and gray) in nanodiscs at 3.6 Å, sharpened with a b-factor of –96 Å2 and contoured at 6.5 σ (upper panel). Close-up of the Ca2+-binding site with two bound Ca2+-ions displayed as blue spheres (lower panel). Cryo-EM density contoured at 7 σ is shown as gray mesh, the backbone is displayed as light green Cα-trace and selected side-chains as sticks. (D–G) Ribbon representation of superpositions with Ca2+-bound structures of nhTMEM16 in nanodiscs: (D) Ca2+-bound open structure in nanodiscs and Ca2+-bound structure in DDM; (E) Ca2+-bound open structure in nanodiscs and Ca2+-bound intermediate structure in nanodiscs; (F) Ca2+-bound intermediate structure in nanodiscs and Ca2+-bound closed structure in nanodiscs; (G) Ca2+-bound closed structure in nanodiscs and Ca2+-free structure in nanodiscs. Selected helices are labeled and views are as in Figure 1.

https://doi.org/10.7554/eLife.44364.012
Figure 3—figure supplement 1
Structure Determination of nhTMEM16 in complex with Ca2+ in nanodiscs.

(A) Representative cryo-EM image and (B) 2D-class averages of vitrified nhTMEM16 in a Ca2+-bound state in lipid nanodiscs. (C) Image processing workflow. The final set of subtracted particles was subjected to a final round of 3D classification disclosing a conformational heterogeneity at the subunit cavity, with classes resembling a well-resolved open, intermediate and closed state of the subunit cavity. Other classes displayed a poorly resolved density for α3 and α4 that likely represent an average of several transition states. Close-up of the subunit cavities show the intermediate model (gray) superimposed on the cryo-EM maps of the respective classes. View as in Figure 3D. (D) FSC plot used for resolution estimation and model validation for each state. Shown are the gold-standard FSC plot between two separately refined half-maps, and the FSC validation curves for FSCsum, FSCwork and FSCfree as described in the Methods.. Thresholds used for FSCsum of 0.5 and for FSC of 0.143 are shown as dashed lines. (E) Sections of the cryo-EM density of the maps superimposed on the corresponding refined models. The models are shown as sticks and structural elements are labelled. The maps were contoured at 4.5 σ.

https://doi.org/10.7554/eLife.44364.013
Figure 3—figure supplement 2
Conformational heterogeneity in the Ca2+-bound data of nhTMEM16 in nanodiscs.

(A–D) Superpositions of the refined and unmasked cryo-EM maps of Ca2+-bound structures of nhTMEM16 in nanodiscs, low-pass filtered at 6 Å. (A) Superposition of the Ca2+-bound open structure in nanodiscs and the Ca2+-bound structure in DDM; (B) the Ca2+-bound open structure in nanodiscs and the Ca2+-bound intermediate structure in nanodiscs; (C) the Ca2+-bound intermediate structure in nanodiscs and the Ca2+-bound closed structure in nanodiscs; (D) the Ca2+-bound closed structure in nanodiscs and the Ca2+-free structure in nanodiscs. A-D, selected helices are labeled, view of upper panel is as in Figure 3D–G. Middle and lower panel show a cross-section through the superposition at the indicated regions depicted in A by * and **.

https://doi.org/10.7554/eLife.44364.014
Figure 3—figure supplement 3
Lipid distribution in the subunit cavity.

(A) Cryo-EM map of Ca2+-bound nhTMEM16 in nanodiscs (gray, contoured at 3.4 σ) with density corresponding to the phospholipid headgroup region of both membrane leaflets in the nanodisc and inside the subunit cavity highlighted in yellow. (B) Ribbon representation of the subunit cavity of the Ca2+-bound nhTMEM16 in nanodiscs (gray) with selected sidechains labelled and depicted as sticks. Unassigned density inside the subunit cavity (contoured at 3.9 σ) is shown in yellow. (C) Cryo-EM map of Ca2+-free nhTMEM16 in nanodiscs (gray, contoured at 3.4 σ) with density of the phospholipid headgroup region of both membrane leaflets in the nanodisc highlighted in green. No residual density is found at the subunit cavity. A,C The refined and unmasked maps were low-pass filtered to 6 Å.

https://doi.org/10.7554/eLife.44364.015
Conformations of the subunit cavity.

Views of the molecular surface of the subunit cavity (top) and structures of α4 and α6 that line the cavity, displayed as Cα-trace with selected sidechains shown as sticks and labeled (bottom). (A) ‘Open state’ as defined in the Ca2+-bound structure in nanodiscs. (B) ‘Intermediate state’ as defined in the Ca2+-bound structure in nanodiscs, (C) ‘Ca2+-bound closed state’ as defined in the Ca2+-bound structure in nanodiscs. (D) ‘Closed state’ as defined by the Ca2+-free structure in nanodiscs. Membrane boundaries are indicated and the region shown in the lower panels is depicted by triangles in the upper panels.

https://doi.org/10.7554/eLife.44364.017
Figure 5 with 1 supplement
Conformational changes.

(A) Ribbon representation of a superposition of the Ca2+-bound ‘open’ (yellow and light gray) and Ca2+-free ‘closed’ (green and dark gray) nhTMEM16 structures in nanodiscs. Selective helices are labeled and the arrows indicate small rearrangements of the cytosolic domain upon Ca2+ release. (B–D) Cα-traces of selected regions of the ‘subunit cavity’ in different conformations as defined by the Ca2+-bound ‘open’ structure in nanodiscs (yellow), the Ca2+-bound ‘intermediate’ structure in nanodiscs (light green) and the Ca2+-free ‘closed’ structure in nanodiscs (dark green). The view in B is as in A and the respective orientations of subsequent panels are indicated. (E) Superposition of α4 in the ‘open’ and ‘closed’ states with residues that act as potential pivots for structural arrangements highlighted in blue.

https://doi.org/10.7554/eLife.44364.018
Figure 5—figure supplement 1
Diameter of the subunit cavity in Ca2+-bound nhTMEM16 structures in nanodiscs.

(A) Pore diameter at the constriction of the subunit cavity in the three conformations of the subunit cavity calculated with HOLE (Smart et al., 1996). (B) View of the constriction of the ‘subunit cavity’ in three different conformations from the extracellular side. The protein is shown as Cα-trace with selected sidechains displayed as sticks and labelled.

https://doi.org/10.7554/eLife.44364.019
Detergent and lipid interactions.

Shown are refined and unmasked cryo-EM density maps low-pass filtered to 6 Å. (A) Map of the Ca2+-bound nhTMEM16 data in detergent contoured at 4 σ; (B,C) Map of the Ca2+-bound nhTMEM16 data in nanodiscs contoured at 3.2 and 1.6 σ; (D) Map of the Ca2+-free nhTMEM16 data in detergent contoured at 4 σ; (E and F), Map of the Ca2+-free nhTMEM16 data in nanodiscs contoured at 3.2 and 1.6 σ. The density corresponding to the detergent micelle or the nanodisc, which is composed of lipids surrounded by the 2N2 belt protein, are colored in orange, yellow, dark green and light green, respectively, density of nhTMEM16 is shown in gray. A,B,D,E show a front view of the dimer similar to Figure 1A and the subunit cavity is indicated by a white arrow. B, E, clipped maps reveal the headgroup regions of both membrane leaflets. C,F, are viewed in direction of the subunit cavity.

https://doi.org/10.7554/eLife.44364.021
Figure 7 with 1 supplement
Functional properties of mutants.

(A) Regions of nhTMEM16 harboring mutated residues. Left, Cα-trace of α4 in ‘open’ (yellow) and ‘closed’ (green) conformations of Ca2+-bound nhTMEM16 in nanodiscs. Right, ion binding site with Ca2+ ions shown in blue. (B–F) Ca2+-dependence of scrambling activity in nhTMEM16-containing proteoliposomes. Traces depict sections of the fluorescence decrease of tail-labeled NBD-PE lipids after addition of dithionite at different Ca2+ concentrations. Data show averages of three technical replicates, errors are s.e.m.. Ca2+ concentrations (μM) are indicated. Full traces are displayed in Figure 7—figure supplement 1. (B) WT, (C) D503A, (D) P341A, (E) G339A, and (F) P332A. (D to F) The traces of WT reconstituted in the same batch of liposomes are shown as dashed lines in the same color as their corresponding conditions of the mutant for comparison. (B to F), The black dashed line refers to the fluorescence decay in protein-free liposomes.

https://doi.org/10.7554/eLife.44364.023
Figure 7—figure supplement 1
Reconstitution efficiency.

(A) Reconstitution efficiency of nhTMEM16 mutants compared to WT (WT1, WT2, WT3) reconstituted in the same batch of solubilized lipids. For analysis, equivalent amounts of liposomes were loaded on SDS-PAGE and detected with an anti-myc antibody detecting a fusion tag on the protein. The positions of molecular weight markers (kDa) are indicated. (B–H) Traces of scrambling experiments displayed in Figure 7. Data show averages of three technical replicates, errors are s.e.m.. Ca2+-dependence of scrambling activity of WT1 (B) and D503A (C) displayed in Figure 7B and C. (D) Ca2+-dependence of scrambling activity of WT2 displayed for comparison in Figure 7D and F. (E) Ca2+-dependence of scrambling activity of WT3 displayed for comparison in Figure 7E. (F) Ca2+-dependence of scrambling activity of P341A displayed for comparison in Figure 7D. (G) Ca2+-dependence of scrambling activity of G339A displayed for comparison in Figure 7E. (H) Ca2+-dependence of scrambling activity of P332A displayed for comparison in Figure 7F. Traces depict fluorescence decrease of tail-labeled NBD-PE lipids after addition of dithionite (#) at different Ca2+ concentrations. Data show averages of three technical replicates. Ca2+ concentrations (μM) are indicated.

https://doi.org/10.7554/eLife.44364.024
Figure 8 with 1 supplement
Activation mechanism.

Scheme of the stepwise activation of nhTMEM16 displaying the equilibrium of states in Ca2+-bound and Ca2+-free conditions. Conformations obtained in this study and their correspondence to distinct states are indicated. Ca2+ and permeating ions are depicted as blue and red spheres, respectively. Phospholipid headgroups are shown as red spheres and acyl chains as gray tails.

https://doi.org/10.7554/eLife.44364.025
Figure 8—figure supplement 1
Activation mechanism.

Scheme of the stepwise activation of nhTMEM16 as shown in Figure 8 with the states displayed by the surface representation of the respective conformation.

https://doi.org/10.7554/eLife.44364.026

Videos

Video 1
Conformational transitions.

Shown is a morph between distinct conformational states obtained for nhTMEM16, namely: the Ca2+-bound ‘open’ state obtained in nanodiscs; the Ca2+-bound ‘intermediate’ state obtained in lipid nanodiscs; the Ca2+-bound ‘closed’ state obtained in lipid nanodiscs; and the Ca2+-free closed state obtained in lipid nanodiscs. Shown is a view of the subunit cavity as depicted in Figure 3 and 4. Ca2+ ions are shown as blue spheres.

https://doi.org/10.7554/eLife.44364.020
Video 2
Micelle and lipid distortion.

Shown are the cryo-EM density maps of nhTMEM16 obtained in detergent in complex with Ca2+ (upper left corner), in detergent in absence of Ca2+ (upper right corner), in lipid nanodiscs in complex with Ca2+ (lower left corner) and in lipid nanodiscs in absence of Ca2+ (lower right corner). The surrounding environment corresponding to the detergent micelle (upper panels) or the lipid nanodiscs (lower panels) are colored respectively, while the rest of the protein is shown in gray. Refined and unmasked cryo-EM maps were low-pass filtered to 6 Å. Transmembrane α-helices 4 and 6 are labeled at the end, indicating the position of the subunit cavity.

https://doi.org/10.7554/eLife.44364.022

Tables

Table 1
Cryo-EM data collection, refinement and validation statistics.
https://doi.org/10.7554/eLife.44364.008
nhTMEM16,
DDM, +Ca2+
(EMDB-4588,
PDB 6QM5)
nhTMEM16,
DDM, -Ca2+
(EMDB-4589,
PDB 6QM6)
nhTMEM16,
2N2, -Ca2+
(EMDB-4587,
PDB 6QM4)
Data collection and processing
Microscope
Camera
Magnification
FEI Talos Arctica
Gatan K2 Summit + GIF
49,407
FEI Talos Arctica
Gatan K2 Summit + GIF
49,407
FEI Talos Arctica
Gatan K2 Summit + GIF
49,407
Voltage (kV)
Exposure time frame/total (s)
Number of frames per image
200
0.15/9
60
200
0.15/9
60
200
0.15/9
60
Electron exposure (e–/Å2)525252
Defocus range (μm)−0.5 to −2.0−0.5 to −2.0−0.5 to −2.0
Pixel size (Å)
Box size (pixels)
1.012
220
1.012
240
1.012
240
Symmetry imposedC2C2C2
Initial particle images (no.)251,693570,2031,379,187
Final particle images (no.)120,086238,070133,961
Map resolution (Å)
0.143 FSC threshold

3.64

3.68

3.79
Map resolution range (Å)3.4–5.03.4–5.03.3–5.0
Refinement
Initial model usedPDB 4WIS6QM56QMB
Model resolution (Å)
FSC threshold

3.6

3.7

3.8
Model resolution range (Å)15–3.615–3.715–3.8
Map sharpening B factor (Å2)−126−147−150
Model composition
Nonhydrogen atoms
Protein residues
Ligands

10874
1346
4

10852
1344
-

10578
1308
-
B factors (Å2)
Protein
Ligand

55.75
33.72

76.42
-

94.09
-
R.m.s. deviations
Bond lengths (Å)
Bond angles (°)

0.007
0.821

0.004
0.835

0.007
0.983
Validation
MolProbity score
Clashscore
Poor rotamers (%)

1.47
4.02
0

1.42
4.35
0

1.53
4.09
0.18
Ramachandran plot
Favored (%)
Allowed (%)
Disallowed (%)

95.92
4.08
0

96.74
3.26
0

95.17
4.83
0
Table 2
Cryo-EM data collection, refinement and validation statistics of the Ca2+ bound nhTMEM16 in nanodiscs.
https://doi.org/10.7554/eLife.44364.016
nhTMEM16,
2N2, +Ca2+open
(EMDB-4592,
PDB 6QM9)
nhTMEM16,
2N2, +Ca2+intermediate closed
(EMDB-4593,
PDB 6QMA)
nhTMEM16,
2N2, +Ca2+closed
(EMDB-4594,
PDB 6QMB)
Data collection and processing
Microscope
Camera
Magnification
FEI Talos Arctica
Gatan K2 Summit + GIF
49,407
Voltage (kV)
Exposure time frame/total (s)
Number of frames per image
200
0.15/9
60
Electron exposure (e–/Å2)52
Defocus range (μm)−0.5 to −2.0
Pixel size (Å)
Box size (pixels)
1.012
240
Symmetry imposedC2
Initial particle images (no.)2,440,110
Final particle images (no.)71,17533,31041,631
Map resolution (Å)
0.143 FSC threshold

3.57

3.68

3.57
Map resolution range (Å)3.4–53.6–53.4–5
Refinement
Initial model used6QM56QMB6QM5
Model resolution (Å)
FSC threshold

3.6

3.7

3.6
Model resolution range (Å)15–3.615–3.715–3.6
Map sharpening B factor (Å2)−114−96−95
Model composition
Nonhydrogen atoms
Protein residues
Ligands

10878
1346
4

10714
1324
4

10696
1322
4
B factors (Å2)
Protein
Ligand

77.93
54.34

84.86
57.57

88.53
67.10
R.m.s. deviations
Bond lengths (Å)
Bond angles (°)

0.005
0.880

0.006
0.872

0.008
0.858
Validation
MolProbity score
Clashscore
Poor rotamers (%)

1.36
3.74
0

1.38
4.69
0.18

1.42
3.90
0
Ramachandran plot
Favored (%)
Allowed (%)
Disallowed (%)

96.82
3.18
0

97.23
2.77
0

96.38
3.62
0
Key resources table
Reagent type
(species) or resource
DesignationSource or referenceIdentifiersAdditional
information
AntibodyMouse monoclonal Anti-c-MycMillipore SigmaCat#M4439; Clone#9E10(1:5000)
AntibodyPeroxidase Affinipuregoat anti-mouse IgGJackson ImmunoresearchCat#115-035-146(1:10000)
Chemical compound, drugn-dodecyl-β-d-maltopyranoside(DDM), SolgradeAnatraceCat#D310S
Chemical
compound, drug
Water for molecular biologyMilliporeH20MB1006
Chemical compound, drugCalcium nitratetetrahydrateMillipore SigmaCat#C4955
Chemical compound, drugSodium chlorideMillipore SigmaCat#71380
Chemical compound, drugMagnesium chlorideFlukaCat#63065
Chemicalcompound, drugHEPESMillipore SigmaCat#H3375
Chemicalcompound, drugEthyleneglycol-bis(2-aminoethylether)-N,N,N′,N′-tetraacetic acidMillipore SigmaCat#03777
Chemicalcompound, drugEthylenediamin
etetraacetic acid
Millipore SigmaCat#E6758
Chemical compound, drugcOmplete, EDTA-freeProtease Inhibitor CocktailRocheCat#5056489001
Chemical compound, drugBiotinMillipore SigmaCat#B4501
Chemical compound, drugD-desthiobiotinMillipore SigmaCat#D1411
Chemical compound, drugGlycerolMillipore SigmaCat#G5516
Chemical
compound, drug
1-palmitoyl-2-oleoyl-glycero-3-phosphocholineAvanti Polar Lipids, IncCat#850457C
Chemical compound, drug1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol)Avanti Polar Lipids, IncCat#840457C
Chemical compound, drugDiethyl etherMillipore SigmaCat#296082
Chemicalcompound, drugE. coli polar lipid extractAvanti Polar Lipids, IncCat#100600C
Chemicalcompound, drugEgg PC, 95%Avanti Polar Lipids, IncCat#131601C
Chemical compound, drug18:1-06:0 NBD-PEAvanti Polar Lipids, IncCat#810155C
Chemicalcompound, drugPotassium chlorideMillipore SigmaCat#746436
Chemicalcompound, drugCHAPSMillipore SigmaCat#C3023
Chemical compound, drugSodium dithioniteMillipore SigmaCat#157953
Chemical compound, drugYeast nitrogen base without amino acidsMillipore SigmaCat#Y0626
Chemicalcompound, drugYeast SyntheticDrop-out MediumSupplements without uracilMillipore SigmaCat#Y1501
Chemicalcompound, drugD-GlucoseApplichemCat#A1422
Chemical compound, drugGalactoseMillipore SigmaCat#G0625
Chemical compound, drugLithium acetateMillipore SigmaCat#L4158
Chemical
compound, drug
PEG3350Millipore SigmaCat#88276
Peptide,recombinant proteinDNAse IAppliChemA3778-0500
Peptide,
recombinant protein
HRV 3C proteaseRaimund Dutzler laboratory
Commercial
assay or kit
Pierce StreptavidinPlus UltraLink ResinThermo Fisher ScientificCat#53117
Commercial
assay or kit
Bio-Beads SM-2
Adsorbents
Bio-RadCat# 1523920
Commercialassay or kitAmicon Ultra-4–100 KDa cutoffEMD MilliporeCat#UFC8100
Commercialassay or kit0.22 μm Ultrafree-MC
Centrifugal Filter
EMD MilliporeCat#UFC30GV
Commercialassay or kitStrep-Tactin Superflow high capacityIBA LifesciencesCat#2-1208-010
Commercial assay or kitSuperdex 200 10/300 GLGE HealthcareCat# 17-5175-01
Commercial assay or kitSuperose 6 10/300 GLGE HealthcareCat#17-5172-01
Strain, strainbackground(S. cerevisiae)FGY217David Drew laboratory
Recombinant DNA reagentnhTMEM16 open reading frameGenScriptPubMed accession number XM_003045982
RecombinantDNA reagentYeast expressionvector withN-terminal streptavidinbinding peptide,Myc tag and 3C protease cleavage siteRaimund Dutzler laboratory
Recombinant DNA reagentMembrane scaffoldprotein (MSP) 2N2Stephen Sligar laboratoryAddgene:Cat#29520
Software, algorithmOnline WEBMAXC calculatorBers et al., 2010http://maxchelator.stanford.edu/webmaxc/webmaxcS.htm
Software, algorithmFocus 1.1.0Biyani et al. (2017)https://focus.c-cina.unibas.ch/about.php
Software,algorithmMotionCorr2 1.1.0Zheng et al. (2017)http://msg.ucsf.edu/em/software/motioncor2.html
Software, algorithmCTFFIND 4.1Rohou and Grigorieff, 2015http://grigoriefflab.janelia.org/ctf
Software, algorithmRelion v 2.1 and 3.0Kimanius et al., 2016https://www2.mrc-lmb.cam.ac.uk/relion/
Software, algorithmPhenix 1.14Adams et al., 2010http://phenix-online.org/
Software, algorithmCoot 0.8.9.1Emsley and Cowtan, 2004https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
Software, algorithmPymol 2.0Schrodinger LLChttps://pymol.org/2/
Software, algorithmChimera 1.12Pettersen et al., 2004https://www.cgl.ucsf.edu/chimera/
Software, algorithmChimeraX 0.6Goddard et al., 2018https://www.rbvi.ucsf.edu/chimerax/
OtherWhatman Nuclepore
Track-Etched Membranes diam. 19 mm, pore size 0.4 μm, polycarbonate
Millipore SigmaCat#WHA800282
OtherHPL6Maximator
OtherFluoromax 4Horiba
Other300 mesh Au 1.2/1.3 cryo-EM gridsQuantifoilCat#N1-C14nAu30-01

Data availability

The three-dimensional cryo-EM density maps of calcium-free nhTMEM16 in detergent and nanodiscs have been deposited in the Electron Microscopy Data Bank under accession numbers EMD-4589 and EMD-4587, respectively. The maps of calcium-bound samples in detergent and calcium-bound open, calcium-bound intermediate and calcium-bound closed in nanodiscs were deposited under accession numbers EMD-4588, EMD-4592, EMD-4593 and EMD-4594, respectively. The deposition includes the cryo-EM maps, both half-maps, the unmasked and unsharpened refined maps and the mask used for final FSC calculation. Coordinates of all models have been deposited in the Protein Data Bank. The accession numbers for calcium-bound and calcium-free models in detergents are 6QM5 and 6QM6, respectively. The accession numbers for calcium-bound open, calcium-bound intermediate, calcium-bound closed and calcium-free models in nanodiscs are 6QM9, 6QMA, 6QMB and 6QM4, respectively.

The following data sets were generated
  1. 1
    Electron Microscopy Data Bank
    1. V Kalienkova
    2. Mosina V Clerico
    3. Bryner Laura
    4. T Oostergetel Gert
    5. Dutzler Raimund
    6. Paulino Cristina
    (2019)
    ID EMD-4587. Cryo-EM structure of calcium-free nhTMEM16 lipid scramblase in nanodisc.
  2. 2
    Protein Data Bank
    1. V Kalienkova
    2. Mosina V Clerico
    3. L Bryner
    4. GT Oostergetel
    5. R Dutzler
    (2019)
    ID 6QM5. Cryo-EM structure of calcium-bound nhTMEM16 lipid scramblase in DDM.
  3. 3
    Protein Data Bank
    1. V Kalienkova
    2. Mosina V Clerico
    3. L Bryner
    4. GT Oostergetel
    5. R Dutzler
    6. C Paulino
    (2019)
    ID 6QM6. Cryo-EM structure of calcium-free nhTMEM16 lipid scramblase in DDM.
  4. 4
    Protein Data Bank
    1. V Kalienkova
    2. Mosina V Clerico
    3. L Bryner
    4. GT Oostergetel
    5. R Dutzler
    6. C Paulino
    (2019)
    ID 6QM9. Cryo-EM structure of calcium-bound nhTMEM16 lipid scramblase in nanodisc (open state).
  5. 5
    Protein Data Bank
    1. V Kalienkova
    2. Mosina V Clerico
    3. L Bryner
    4. GT Oostergetel
    5. R Dutzler
    6. C Paulino
    (2019)
    ID 6QMA. Cryo-EM structure of calcium-bound nhTMEM16 lipid scramblase in nanodisc (intermediate state).
  6. 6
    Protein Data Bank
    1. V Kalienkova
    2. Mosina V Clerico
    3. L Bryner
    4. GT Oostergetel
    5. R Dutzler
    6. C Paulino
    (2019)
    ID 6QMB. Cryo-EM structure of calcium-bound nhTMEM16 lipid scramblase in nanodisc (closed state).
  7. 7
    Protein Data Bank
    1. V Kalienkova
    2. Mosina V Clerico
    3. L Bryner
    4. GT Oostergetel
    5. R Dutzler
    6. C Paulino
    (2019)
    ID 6QM4. Cryo-EM structure of calcium-free nhTMEM16 lipid scramblase in nanodisc.
  8. 8
    Electron Microscopy Data Bank
    1. V Kalienkova
    2. Mosina V Clerico
    3. L Bryner
    4. GT Oostergetel
    5. R Dutzler
    6. C Paulino
    (2019)
    ID EMD-4588. Cryo-EM structure of calcium-bound nhTMEM16 lipid scramblase in DDM.
  9. 9
    Electron Microscopy Data Bank
    1. V Kalienkova
    2. Mosina V Clerico
    3. L Bryner
    4. GT Oostergetel
    5. R Dutzler
    6. C Paulino
    (2019)
    ID EMD-4589. Cryo-EM structure of calcium-free nhTMEM16 lipid scramblase in DDM.
  10. 10
    Electron Microscopy Data Bank
    1. V Kalienkova
    2. Mosina V Clerico
    3. L Bryner
    4. GT Oostergetel
    5. R Dutzler
    6. C Paulino
    (2019)
    ID EMD-4592. Cryo-EM structure of calcium-bound nhTMEM16 lipid scramblase in nanodisc (open state).
  11. 11
    Electron Microscopy Data Bank
    1. V Kalienkova
    2. Mosina V Clerico
    3. L Bryner
    4. GT Oostergetel
    5. R Dutzler
    6. C Paulino
    (2019)
    ID EMD-4593. Cryo-EM structure of calcium-bound nhTMEM16 lipid scramblase in nanodisc (intermediate state).
  12. 12
    Electron Microscopy Data Bank
    1. V Kalienkova
    2. Mosina V Clerico
    3. L Bryner
    4. GT Oostergetel
    5. R Dutzler
    6. C Paulino
    (2019)
    ID EMD-4594. Cryo-EM structure of calcium-bound nhTMEM16 lipid scramblase in nanodisc (closed state).

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