2024-11-06 REL PDBe PDBe PDBe 2019-10-28 2019-11-20 2019-11-20 2024-11-06 Wellcome Trust 106169/Z/14/Z United Kingdom CryoEM structure of human polycystin-2/PKD2 in UDM supplemented with PI(3,5)P2 Wang Q Pike ACW ION CHANNEL, TRANSIENT RECEPTOR POTENTIAL CHANNEL, POLYCYSTIC KIDNEY DISEASE, Structural Genomics, Structural Genomics Consortium, SGC, MEMBRANE PROTEIN Wang Q Corey RA Hedger G Aryal P Grieben M Nasrallah C Baronina A Pike ACW Shi J Carpenter EP Sansom MSP Lipid Interactions of a Ciliary Membrane TRP Channel: Simulation and Structural Studies of Polycystin-2. Structure UK 28 169 184.e5 2020 31806353 doi:10.1016/j.str.2019.11.005 0969-2126 2005 STRUE6 6t9o FULLOVERLAP Polycystin-2 channel tetramer Polycystin-2 channel tetramer 0 1 Homo sapiens 0.256 Polycystin-2 Homo sapiens 0.063986668 4 Spodoptera frugiperda LEVO MPRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVS KTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKE CYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATF IDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYF RSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTM SQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTT FVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKNTVDAENLYFQ Q13563 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 8 NAG CHOLESTEROL 0.000386654 4 CLR UNDECYL-MALTOSIDE 0.000496589 20 UMQ CALCIUM ION 4.0078e-05 1 CA singleParticle particle 3.8 7.5 20.0 C8H18N2O4S HEPES 200.0 NaCl Sodium chloride 20.0 CaCl2 Calcium chloride 0.035 C23H44O11 N-undecyl-beta-D-maltopyranoside Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE AIR ETHANE 100 278 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 1.0 3.1 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 25
eBIC Krios3
GATAN K2 SUMMIT (4k x 4k) COUNTING 1-32 1 3353 7.0 42.0 1 163983
ab-initio model generated in RELION
 1 C4 3.39 FSC 0.143 CUT-OFF RELION 3
Final autorefinement was carried out in RELION without masking giving an unmasked (FSC 0.143) resolution of 3.82. Masking to remove the detergent micelle gave a final resolution of 3.39A
37297 MAXIMUM LIKELIHOOD RELION 3 MAXIMUM LIKELIHOOD RELION 3 10 8200.0 RELION 3
Final 3D classification carried out in 10 classes with no image alignment after 3D autorefinement with C4 symmetry
 emd_10419.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 220 220 220 0 0 0 220 220 220 179.51999 179.51999 179.51999 90.0 90.0 90.0 X Y Z -0.05114744 0.08678348 0.00011854263 0.004649328 0.8159999 0.8159999 0.8159999 0.012 AUTHOR RELION postprocessed map sharpened with a bfactor of -109A**2 and filtered to 3.39A AB INITIO MODEL REAL 109.0 emd_10419_msk_1.map emd_10419_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 220 220 220 0 0 0 220 220 220 179.51999 179.51999 179.51999 90.0 90.0 90.0 X Y Z -0.01079479 0.030332524 0.000104758095 0.002263633 0.8159999 0.8159999 0.8159999 AUTHOR RELION autorefined map, unsharpened, unfiltered emd_10419_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 220 220 220 0 0 0 220 220 220 179.51999 179.51999 179.51999 90.0 90.0 90.0 X Y Z -0.030443927 0.04113834 0.00011984789 0.0032635983 0.8159999 0.8159999 0.8159999 AUTHOR Refine3D half-map2 emd_10419_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 220 220 220 0 0 0 220 220 220 179.51999 179.51999 179.51999 90.0 90.0 90.0 X Y Z -0.027595043 0.039361306 0.00011723736 0.0032824082 0.8159999 0.8159999 0.8159999 AUTHOR Refine3D half-map1