2024-10-09 REL PDBe PDBe PDBe 2017-09-08 2017-09-20 2017-12-20 2024-10-09 University of Zurich FK-16-036 Switzerland European Research Council 339116AnoBest Switzerland Paulino C Kalienkova V TMEM16 family, ion channel, membrane protein, cryo-EM Paulino C Kalienkova V Lam AKM Neldner Y Dutzler R Nature UK 552 421 425 2017 29236691 doi:10.1038/nature24652 1476-4687 0006 NATUAS EMD-3861 other EM volume

structure of the calcium-free mTMEM16A chloride channel at 4.06 A

5oyb FULLOVERLAP mTMEM16A with calcium ions bound mTMEM16A with calcium ions bound 0 1

calcium-activated chloride channel

Mus musculus 0.110916 Anoctamin-1 Mus musculus 0.111058992 2 Homo sapiens LEVO MRVPEKYSTLPAEDRSVHIVNICAIEDLGYLPSEGTLLNSLSVDPDAECKYGLYFRDGKRKVDYILVYHHKRASGSRTLA RRGLQNDMVLGTRSVRQDQPLPGKGSPVDAGSPEVPMDYHEDDKRFRREEYEGNLLEAGLELENDEDTKIHGVGFVKIHA PWHVLCREAEFLKLKMPTKKVYHISETRGLLKTINSVLQKITDPIQPKVAEHRPQTTKRLSYPFSREKQHLFDLTDRDSF FDSKTRSTIVYEILKRTTCTKAKYSMGITSLLANGVYSAAYPLHDGDYEGDNVEFNDRKLLYEEWASYGVFYKYQPIDLV RKYFGEKVGLYFAWLGAYTQMLIPASIVGVIVFLYGCATVDENIPSMEMCDQRYNITMCPLCDKTCSYWKMSSACATARA SHLFDNPATVFFSVFMALWAATFMEHWKRKQMRLNYRWDLTGFEEEEEAVKDHPRAEYEARVLEKSLRKESRNKETDKVK LTWRDRFPAYFTNLVSIIFMIAVTFAIVLGVIIYRISTAAALAMNSSPSVRSNIRVTVTATAVIINLVVIILLDEVYGCI ARWLTKIEVPKTEKSFEERLTFKAFLLKFVNSYTPIFYVAFFKGRFVGRPGDYVYIFRSFRMEECAPGGCLMELCIQLSI IMLGKQLIQNNLFEIGIPKMKKFIRYLKLRRQSPSDREEYVKRKQRYEVDFNLEPFAGLTPEYMEMIIQFGFVTLFVASF PLAPLFALLNNIIEIRLDAKKFVTELRRPVAIRAKDIGIWYNILRGVGKLAVIINAFVISFTSDFIPRLVYLYMYSQNGT MHGFVNHTLSSFNVSDFQNGTAPNDPLDLGYEVQICRYKDYREPPWSEHKYDISKDFWAVLAARLAFVIVFQNLVMFMSD FVDWVIPDIPKDISQQIHKEKVLMVELFMREEQGKQQLLDTWMEKEKPRDVPCNNHSPTTHPEAGDGSPVPSYEYHGDAL Q8BHY3 CALCIUM ION 4.0078e-05 4 CA singleParticle particle 3.5 7.5 20.0 Hepes

20 mM Hepes 150 mM NaCl 0.5 mM CaCl2 <0.12% digitonin

Quantifoil R1.2/1.3 GOLD 200 CARBON HOLEY GLOW DISCHARGE 30 ETHANE 100 288 FEI VITROBOT MARK IV

2 ul sample volume 2-4 sec blotting time.

full-length (wild-type isoform ac) deglycosylated mTMEM16A in presence of 0.5mM CaCl2

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 0.5 0.5 3.0 3.0 46511.0 46511.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 80.0 100.0 In-column Omega Filter -10 +10 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 7420 7676 1-80 3 4343 10.0 80.0

Data were collected in an automated fashion using SerialEM47 on a K2 Summit detector (Gatan). For the dataset in presence of calcium ions, cryo-EM images were collected at a pixel size of 0.5375A in super-resolution mode, a defocus range of -0.5 to -3.0 um, an exposure time of 10 sec and a sub-frame exposure time of 125 ms (80 frames) with an approximate electron dose of 1 e-/A2/frame. An extensive effort was made for this dataset to screen different areas within the grid and only regions that provided an estimated resolution of the CTF fit of better than 4A were selected for data collection. The total accumulated dose on the specimen level was approximately 80 e-/A2.

1

Fourier cropping (final pixel size 1.075 A), motion correction and dose-weighting of frames were performed by MotionCor2

629679

For the dataset collected in presence of calcium ions a total of 4,342 dose-fractionated super-resolution images were recorded, 2 x 2 down-sampled by Fourier cropping (final pixel size 1.075A) and subjected to motion correction and dose-weighting of frames by MotionCor248. The contrast transfer function (CTF) parameters were estimated on the movie frames by ctffind4.149. Images showing a strong drift, higher defocus than -3.0 um or a bad CTF estimation were discarded, resulting in 2,997 images used for further analysis with the software package RELION2.1b150. Particles were picked automatically using 2D class averages from the previously obtained TMEM16A cryo-EM map as reference26 providing an initial set of 629,679 particles. After extraction with a box size of 300 pixels, false positives were eliminated manually or through a first round of 2D classification, resulting in 368,162 particles that were further subjected to several rounds of 2D classification to remove particles belonging to low-abundance classes. The remaining 252,577 particles were sorted during 3D Classification, a C2 symmetry was imposed and the low-resolution TMEM16A cryo-EM map (EMD-3658) was used as initial model. The best class, comprising 147,368 particles from a total of 2012 images, was subjected to auto-refinement and particle polishing in RELION, with a running average window of 5, a standard deviation of 1 pixel on translations and 200 pixels on particle distance. The final polished and auto-refined map used for model building had a resolution of 4.6A before masking and 3.75A after masking and was sharpened using an isotropic b-factor of -1063A2

5NL2 C2 3.75 FSC 0.143 CUT-OFF RELION 2.1b1 147368 ANGULAR RECONSTITUTION RELION 21b1 ANGULAR RECONSTITUTION RELION 2.1b1 RELION 2.1b1 RIGID BODY FIT emd_3860_msk_1.map emd_3860_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 322.5 322.5 322.5 90.0 90.0 90.0 X Y Z -0.07279356 0.12662388 0.00008710323 0.004395553 1.075 1.075 1.075 AUTHOR ::::EMDATABANK.org::::D_1200006568:::: None emd_3860_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 322.5 322.5 322.5 90.0 90.0 90.0 X Y Z -0.0087958705 0.023413412 0.000010159953 0.001291705 1.075 1.075 1.075 AUTHOR ::::EMDATABANK.org::::D_1200006568:::: cryo-EM half map 2 of the ion channel TMEM16A from mouse in presence of calcium ions emd_3860_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 322.5 322.5 322.5 90.0 90.0 90.0 X Y Z -0.0093410695 0.024025878 0.00008096233 0.001292658 1.075 1.075 1.075 AUTHOR ::::EMDATABANK.org::::D_1200006568:::: cryo-EM half map 1 of the ion channel TMEM16A from mouse in presence of calcium ions