2024-07-10 REL PDBe PDBe PDBe 2021-01-09 2021-01-27 2021-01-27 2024-07-10 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM108043 United States European Research Council (ERC) 637372 Denmark Danish Council for Independent Research DFF-8021-00161 Denmark Cryo-EM Structure of KdpFABC in E1 state with K Sweet ME Larsen C P-type ATPase, ATP-dependent potassium pump, MEMBRANE PROTEIN Sweet ME Larsen C Zhang X Schlame M Pedersen BP Stokes DL Structural basis for potassium transport in prokaryotes by KdpFABC. Proc.Natl.Acad.Sci.USA US 118 2021 34272288 doi:10.1073/pnas.2105195118 1091-6490 0040 PNASA6 7bh1 FULLOVERLAP KdpFABC in E1 apo state KdpFABC in E1 apo state 0 1 2 3 4
KdpFABC complex solublized in decyl maltopyranoside (DM) detergent.
Escherichia coli K-12 .16 Potassium-transporting ATPase potassium-binding subunit Escherichia coli K-12 0.059247684 1 Escherichia coli LEVO MAAQGFLLIATFLLVLMVLARPLGSGLARLINDIPLPGTTGVERVLFRALGVSDREMNWKQYLCAILGLNMLGLAVLFFM LLGQHYLPLNPQQLPGLSWDLALNTAVSFVTNTNWRSYSGETTLSYFSQMAGLTVQNFLSAASGIAVIFALIRAFTRQSM STLGNAWVDLLRITLWVLVPVALLIALFFIQQGALQNFLPYQAVNTVEGAQQLLPMGPVASQEAIKMLGTNGGGFFNANS SHPFENPTALTNFVQMLAIFLIPTALCFAFGEVMGDRRQGRMLLWAMSVIFVICVGVVMWAEVQGNPHLLALGTDSSINM EGKESRFGVLVSSLFAVVTTAASCGAVIAMHDSFTALGGMVPMWLMQIGEVVFGGVGSGLYGMMLFVLLAVFIAGLMIGR TPEYLGKKIDVREMKLTALAILVTPTLVLMGAALAMMTDAGRSAMLNPGPHGFSEVLYAVSSAANNNGSAFAGLSANSPF WNCLLAFCMFVGRFGVIIPVMAIAGSLVSKKSQAASSGTLPTHGPLFVGLLIGTVLLVGALTFIPALALGPVAEYLS P03959 Potassium-transporting ATPase ATP-binding subunit Escherichia coli K-12 0.072251867 1 Escherichia coli LEVO MSRKQLALFEPTLVVQALKEAVKKLNPQAQWRNPVMFIVWIGSLLTTCISIAMASGAMPGNALFSAAISGWLWITVLFAN FAEALAEGRSKAQANSLKGVKKTAFARKLREPKYGAAADKVPADQLRKGDIVLVEAGDIIPCDGEVIEGGASVDESAITG EAAPVIRESGGDFASVTGGTRILSDWLVIECSVNPGETFLDRMIAMVEGAQRRKTPNEIALTILLIALTIVFLLATATLW PFSAWGGNAVSVTVLVALLVCLIPTTIGGLLSAIGVAGMSRMLGANVIATSGRAVEAAGDVDVLLLDKTGTITLGNRQAS EFIPAQGVDEKTLADAAQLASLADETPEGRSIVILAKQRFNLRERDVQSLHATFVPFTAQSRMSGINIDNRMIRKGSVDA IRRHVEANGGHFPTDVDQKVDQVARQGATPLVVVEGSRVLGVIALKDIVKGGIKERFAQLRKMGIKTVMITGDNRLTAAA IAAEAGVDDFLAEATPEAKLALIRQYQAEGRLVAMTGDGTNDAPALAQADVAVAMNSGTQAAKEAGNMVDLDSNPTKLIE VVHIGKQMLMTRGSLTTFSIANDVAKYFAIIPAAFAATYPQLNALNIMCLHSPDSAILSAVIFNALIIVFLIPLALKGVS YKPLTASAMLRRNLWIYGLGGLLVPFIGIKVIDLLLTVCGLV P03960 7.2.2.6 Potassium-transporting ATPase KdpC subunit Escherichia coli K-12 0.022299225 1 Escherichia coli LEVO MSGLRPALSTFIFLLLITGGVYPLLTTVLGQWWFPWQANGSLIREGDTVRGSALIGQNFTGNGYFHGRPSATAEMPYNPQ ASGGSNLAVSNPELDKLIAARVAALRAANPDASASVPVELVTASASGLDNNITPQAAAWQIPRVAKARNLSVEQLTQLIA KYSQQPLVKYIGQPVVNIVELNLALDKLDEGTGLVPRGSSHHHHHHHH P03961 Potassium-transporting ATPase KdpF subunit Escherichia coli K-12 0.0030717139999999997 1 Escherichia coli LEVO MSAGVITGVLLVFLLLGYLVYALINAEAF P36937 POTASSIUM ION 3.9098e-05 1 K (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate 0.0007179959999999999 1 9Y0 water 1.8015e-05 6 HOH singleParticle particle 4.5 7.5 25.0 (HOCH2)3CNH2 tris(hydroxymethyl)aminomethane 100.0 KCl potassium chloride 5.0 MgCl2 magnesium chloride 1.0 C9H15O6P tris(2-carboxyethyl)phosphine 1.5 C22H42O11 decyl maltopyranoside 100.0 NaCl sodium chloride UltrAuFoil R1.2/1.3 GOLD 300 GOLD HOLEY ARRAY 50.0 GLOW DISCHARGE AIR
PELCO easiGlow Glow Discharge Cleaning System used for glow discharge with default settings.
 ETHANE 100 277 FEI VITROBOT MARK IV
3 uL of protein mixture applied to grid. Blot time 4 seconds, blot force 0, no wait before plunging..
DM-solublized KdpFABC complex purified through SEC the same day as grid freezing. Peak fraction diluted to 4.5 mg/mL prior to application to grid.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 1.0 2.2 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 77.0 77.0 GIF Bioquantum 20 GATAN K2 QUANTUM (4k x 4k) 3838 3710 1-50 1 2096 10.0 50.0 1 376593
template based picker
ab initio
 1 C1 FOURIER SPACE 3.38 FSC 0.143 CUT-OFF cryoSPARC 2.9.0 202071 RANDOM ASSIGNMENT cryoSPARC 2.9.0 MAXIMUM LIKELIHOOD cryoSPARC 2.9.0
non-uniform refinement
 3 cryoSPARC 2.9.0
hetero-refinement
 emd_12185.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 331.19998 331.19998 331.19998 90.0 90.0 90.0 X Y Z -2.6934812 4.3302126 0.0023455939 0.088438205 1.035 1.035 1.035 0.6 AUTHOR For model building, original map is tranformed by zflip 5MRW PDB experimental model RIGID BODY FIT Correlation coefficient REAL emd_12185_msk_1.map emd_12185_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 331.19998 331.19998 331.19998 90.0 90.0 90.0 X Y Z -2.0761602 2.2221837 0.0024875319 0.23399591 1.035 1.035 1.035 AUTHOR Half Map A from cryoSPARC non-linear refinement emd_12185_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 331.19998 331.19998 331.19998 90.0 90.0 90.0 X Y Z -1.8885068 2.2549303 0.0024807863 0.2339972 1.035 1.035 1.035 AUTHOR Half Map B from cryoSPARC non-linear refinement