2024-11-06 REL PDBe PDBe PDBe 2017-10-08 2017-12-20 2017-12-27 2024-11-06 Swiss National Science Foundation 315230_146929, 205320_144427 Switzerland Kowal J Biyani N MloK1, MlotiK1, potassium channel, CNBD, cytoplasmic domains, PCO refinement, MEMBRANE PROTEIN Kowal J Biyani N Chami M Scherer S Rzepiela AJ Baumgartner P Upadhyay V Nimigean CM Stahlberg H Structure UK 26 20 27.e3 2018 29249605 doi:10.1016/j.str.2017.11.012 1878-4186 2005 STRUE6 6eo1 FULLOVERLAP MloK1 tetramer MloK1 tetramer 0 1

Cyclic nucleotide-modulated potassium channel in the presence of cAMP ligand, reconstituted into 2D lipid membrane crystals.

Mesorhizobium loti Membrane 0.148 Cyclic nucleotide-gated potassium channel mll3241 Mesorhizobium loti MAFF303099 Membrane 0.037766297 4 Escherichia coli BL21(DE3) LEVO MSVLPFLRIYAPLNAVLAAPGLLAVAALTIPDMSGRSRLALAALLAVIWGAYLLQLAATLLKRRAGVVRDRTPKIAIDVL AVLVPLAAFLLDGSPDWSLYCAVWLLKPLRDSTFFPVLGRVLANEARNLIGVTTLFGVVLFAVALAAYVIERDIQPEKFG SIPQAMWWAVVTLSTTGYGDTIPQSFAGRVLAGAVMMSGIGIFGLWAGILATGFYQEVRRGDFVRNWQLVAAVPLFQKLG PAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPVELGPGAFFGEMALISGEPRSATVSAATTVSLL SLHSADFQMLCSSSPEIAEIFRKTALERRGAAASA Q98GN8 POTASSIUM ION 3.9098e-05 2 K electronCrystallography twoDArray 0.7 7.6

20 mM KCl, 20 mM Tris-HCl pH 7.6, 1 mM BaCl2, 1 mM EDTA, 0.2 mM cAMP

Quantifoil R3.5/1 COPPER 400 CARBON CONTINUOUS 3.0 GLOW DISCHARGE 30 AIR ETHANE 90 293 FEI VITROBOT MARK IV

3.5 second-blotting.

0.8 E.coli polar lipids dialysis buttons dialysis buffer 293.0 5.0

DM solubilized MloK1 sample was mixed with E. coli polar lipid extract (Avanti Polar Lipids) at a lipid to protein ratio of 0.8 and dialyzed against detergent free buffer. 2D crystals of the lipid embedded protein were obtained within 5 days.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 0.75 4.3 50000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Quantum LS 0 20

pixel size 1.3 A/pix

GATAN K2 SUMMIT (4k x 4k) COUNTING 30 346 16.0 45.0

Each image was dose-fractionated in 40 frames (16 sec in total, 0.4-sec frames). The dose rate was set to ~5 counts/sec/physical-pixel (~2.8 e-/s/A2)leading to a total dose of ~45 e-/A2. Pixel size was 1.3A/pix.

800 0.0 55.0 1

Gatan Quantum-LS energy filter, with K2 Summit detector

4.5 OTHER 135 135 200 135 90 P 4 21 2 Arheit et al., 2013a; Arheit et al., 2013b; Arheit et al., 2013c; Gipson et al., 2008; Gipson et al., 2007; Gipson et al., 2011; Biyani et al., 2017 6361 6901357 100.0 99.0 99.0 99 99.0 99 4.5 4.5 6.0 6901357 99.0 100.0 300.0

Image processing was done with FOCUS (formerly 2dx), available at FOCUS-EM.org. Arheit et al., 2013a; Arheit et al., 2013b; Arheit et al., 2013c; Gipson et al., 2008; Gipson et al., 2007; Gipson et al., 2011; Biyani et al., 2017. Rsym, Rmerge, and phase errors are not available.

4CHV A 1-355 PDB experimental model FLEXIBLE FIT

The initial model was obtained using Modeller (Sali and Blundell, 1993); in particular, the missing fragments were generated for the previously published PDB 4CHV model. This starting model was refined using the Rosetta for cryo-EM package (DiMaio et al., 2015). The symmetry of the channel was restrained during optimization runs (performed following the package tutorial (Wang and DiMaio,2015)). A model with a high fit score to the cryo-EM map and a low energy, as defined by the Rosetta force field, was selected from 100 Rosetta models generated and refined further. Several rounds of manual refinement with Coot (Emsley et al.,2010) and global optimization with Phenix (real_space_refine method (Afonine et al., 2013)) were carried out. Secondary structure constraints were imposed to stabilize the fold of helices and b-sheets during the global optimization.

fit energy REAL emd_3907_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 140 140 140 -9 -9 30 140 140 140 133.7 133.7 146.29999 90.0 90.0 90.0 X Y Z -0.057985876 0.08118846 -0.00001783505 0.007740139 0.955 0.955 1.045 AUTHOR ::::EMDATABANK.org::::EMD-3907:::: Back-projected 3D volume of MloK1 with cAMP