2024-11-20 REL PDBe PDBe PDBe 2023-01-20 2024-04-10 2024-04-10 2024-11-20 Wellcome Trust 202231/Z/16/Z United Kingdom Medical Research Council (MRC, United Kingdom) MC_UP_1201/31 United Kingdom In situ structure of the Nitrosopumilus maritimus S-layer - Two-fold symmetry (C2) von Kuegelgen A Bharat T Nmar_1547 S-layer, STRUCTURAL PROTEIN von Kugelgen A Cassidy CK van Dorst S Pagani LL Batters C Ford Z Lowe J Alva V Stansfeld PJ Bharat TAM Membraneless channels sieve cations in ammonia-oxidizing marine archaea. Nature UK 630 230 236 2024 38811725 doi:10.1038/s41586-024-07462-5 1476-4687 0006 NATUAS 8c8n FULLOVERLAP Nitrosopumilus maritimus S-layer Nitrosopumilus maritimus S-layer 0 1
Nitrosopumilus maritimus S-layer C2 symmetrised
Nitrosopumilus maritimus SCM1 SCM1 extracellular Cell surface protein Nitrosopumilus maritimus SCM1 SCM1 0.18315599999999999 6 LEVO MNNEIGRKITSLTLMTIMVAGGLTFAIPGVMPEAMAANANLFVSAENSQFDNYMSGPQVIEVVVIDSDINDTDEAKGEPD VTVNGKVLRMVQAVDGNWYGYFADRDQAQIADSTATTADSGLDFGVFCASSSGTAALGFSTTETDGIAIPITIANATATG NGTQTGSSSGGAITTTCAANTLDASTANGTINVVREAKDPVAASGSVSVGQIGLKNGTANSGPNWPFIQLYELNPTGNVV VQYNKGGGVQSTTLTFDTVDQFAELSLDRTVFPRVSQVHATITDLWLNIDPTDEDSWTFATNTKNTTSSFNVDTFYQVFD ENGASGGSALTLRTTLSSLMCEDNCVLTLDVDAQSSGTPVVTIQDNGDSILTQLNASSNTNANNASAFGISTETAKLGTG SIPVTITEQGPNSGVFGTYDESDKSVLKITDNAKRGTSASLDYNETPQTILVGFSFASIDIQPVTDEWTSGQEIPVVIVD ADQNKNSRADEDLDLNNPDVTLIPALRTGDPFTIDEGGTPSLIFTNGTNGDDSIFDTGAINNTSAGQVGNFTLNINVTRF SSATNITSTESIDTFSKRLISAQTANSSANFDVDFAIIDLGSATLETLKETVVDEDNTAVGFNFFNYDVRSLGADTVSIA LLNTTGNILPWVNNDTRNVDKNNAILLVSNSTNSQAYVDLTNAVSDAVYGSTNTDSNVNIGFAMYFTGVGDLAAKEVIVM DFFSFGFTDDGVQSSERFANQIIRIEAEETGDNTSTFEGSLEYVMVNQINIQDAGTFSGITPIADDPSFIVIEDLTDEDA PRVNYNDLGADGVTTPVSDQEEAPSHSGVVSLNADSYKIADTVVITVEDLDLNVDSDLIDIFTVVSDNSKATDDAVGSAT TQSLSFGELGRLLDVTFDDVIWSTPDGANNTATGNDSDTCSTELSNAGITDTGLGATGFTLVETGAATGVFVGDFQIPSF WCRVSDTTTTPYTYAGDEETTTGLDIEVNYVDFRDASGEIVEVGDSAGVRANTGSVSLDRTVYPVPFGTIADSSKAANAA PNGRSVFPIHATGITSTIDSTEELPTGDLTIHVRINDPDFDENPAGEDAMDQDNALKISVIRGSDSVVLGYAGASERTGK IDVGGNNGTISNIRSFGEMDEIAPDAGIFELDVNIKFTDGPASAQCNSHDTLYTALDGTTGKADTNRFDDGAASGQEYCI LQGDILQVEYTDPADASGDANTVTDSATFDLRNGVLQSDKSVYIIGSDMILTLIEPDFDLDNDSAETYDLDLIEWDSDAA TTTMGNKGVTGAAAAFDPEPTDFRETGDSTGIFQIVIEIPESLSNDKLERGEEIILEYTDWGPSGSDYVGDEDEDVNLTI YTSNFGATVELDQKVYSWTDKVYITIVAPDHNFDSDLVDEIGETDSDPIKVSTRGFDLDNYKLVETGTDTGIFTGEVILT GFTAHDADGDGNTGDATGTTSGSGPTDGLLATDDDDGLTVSFEFSEDETIVGSALIRWNIGEVQWLEASYPASGTGVVRV IDPDMNLDPEAVDNFEVDVWSDSDAGGIDLTVTETNEATGIFEGTVFFTTLDESSGHRLRVSEGDTVTAEYEDNTLPDPY TTADELDITATSLIGTVVPPLERAPAANLRTVDAFGNSLDSVSVDQQVQISADLANGQDREQSFAYLVQIQDANGVTVSL AWITGSLSSGQSFSPALSWIPTEAGTYTATAFVWESVDNPTALSPPVSTTVNVS A9A4Y9 subtomogramAveraging cell 7.4 10.0 C8H18N2O4S HEPES 444.9 NaCl NaCl 20.286 MgSO4 MgSO4 24.59 MgCl2 MgCl2 10.2 CaCl2 CaCl2 1.0 NH4Cl NH4Cl 14.696 KH2PO4 KH2PO4 7.5 FeNaC10H12N2O8 FeNaEDTA 0.5 H3BO3 H3BO3 0.5 MnCl2 MnCl2 0.8 CoCl2 CoCl2 0.1 NiCl2 NiCl2 0.01 CuCl2 CuCl2 0.5 ZnSO4 ZnSO4 0.15 Na2MoO4 Na2MoO4
Modified Syntheic Crenarchaeota medium
 Quantifoil R2/2 COPPER/RHODIUM 200 CARBON HOLEY ARRAY GLOW DISCHARGE AIR
15 mA
 NITROGEN 100 283.15 FEI VITROBOT MARK IV
absorption for 60 sec and blotted for 5 sec with blot force -10.
Nitrosopumilus maritimus cells
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 2.0 2.0 5.0 5.0 105000.0 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 70.0 70.0 not used not used GIF Quantum LS 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 1-10 1 0.9 2.96
Dose-symmetric tilt scheme (Hagen et al)
 1 C2 FOURIER SPACE 3.4 FSC 0.143 CUT-OFF RELION 4.0.0 108621 153 138532 None RELION 4.0.0 RELION 4.0.0 MAXIMUM LIKELIHOOD RELION 4.0.0
RELION 4.0.0
 emd_16487.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 265.4 265.4 265.4 90.0 90.0 90.0 X Y Z -0.12001334 0.20476614 -0.00020214982 0.0103099905 1.327 1.327 1.327 0.02557 AUTHOR PostProcessed map with B-factor sharpening AB INITIO MODEL Best Fit RECIPROCAL 66.189999999999998 emd_16487_msk_1.map emd_16487_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 265.4 265.4 265.4 90.0 90.0 90.0 X Y Z -0.07563573 0.13946751 -0.00020210457 0.00756437 1.327 1.327 1.327 AUTHOR Full Refine3D map non-sharpened emd_16487_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 265.4 265.4 265.4 90.0 90.0 90.0 X Y Z -0.11751633 0.17915952 -0.00020511562 0.011631127 1.327 1.327 1.327 AUTHOR Half 2 emd_16487_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 265.4 265.4 265.4 90.0 90.0 90.0 X Y Z -0.115450196 0.17596377 -0.00019918403 0.011649201 1.327 1.327 1.327 AUTHOR Half 1