2024-10-16 REL PDBe PDBe PDBe 2023-01-20 2024-04-10 2024-04-10 2024-10-16 Wellcome Trust 202231/Z/16/Z United Kingdom Medical Research Council (MRC, United Kingdom) MC_UP_1201/31 United Kingdom 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 Nature UK 630 230 236 2024 38811725 doi:10.1038/s41586-024-07462-5 1476-4687 0006 NATUAS EMD-16483 other EM volume

Consensus Map

EMD-16482 other EM volume

Focused Refinement

8c8m FULLOVERLAP Nitrosopumilus maritimus S-layer Nitrosopumilus maritimus S-layer 0 1

Nitrosopumilus maritimus S-layer composite map between two and six-fold symmetrised maps

Nitrosopumilus maritimus SCM1 SCM1 extracellular Cell surface protein Nitrosopumilus maritimus SCM1 SCM1 0.18315599999999999

In-vitro isolated S-layer

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 singleParticle twoDArray 7.5 50.0 C8H18N2O4S HEPES 500.0 NaCl NaCl 50.0 MgCl2 MgCl2 10.0 CaCl2 CaCl2

50 mM HEPES/NaOH pH=7.5, 500 mM NaCl, 50 mM MgCl2, 10 mM CaCl2

Quantifoil R2/2 COPPER/RHODIUM 200 CARBON HOLEY ARRAY GLOW DISCHARGE 20 AIR

15 mA

NITROGEN 100 283.15 FEI VITROBOT MARK IV

absorption for 60 sec and blotted for 5 sec with blot force -10.

In vitro isolate S-layer cell envelopes

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 2.0 2.0 5.0 5.0 81000.0 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 70.0 70.0 not used not used GIF Quantum LS 20 GATAN K3 BIOQUANTUM (6k x 4k) 5760 4092 3 12557 4.2 48.5

collected over three sessions one with session with the stage tilted by 33 degrees

1

Movies collected at the scope were clustered into optics groups based on the XML meta-data of the data-collection software EPU (Thermo Fisher Scientific) using a k-means algorithm implemented in EPU_group_AFIS (https://github.com/DustinMorado/EPU_group_AFIS). Imported movies were motion-corrected, dose-weighted, and Fourier cropped (2x) with MotionCor2 implemented in RELION-3.1. Contrast transfer functions (CTFs) of the resulting motion-corrected micrographs were estimated using CTFFIND4.

1971908

Initially, side views of S-layer sheets were first manually picked along the edge of the lattice using the helical picking tab in RELION while setting the helical rise to 60 angstrom. Top and tilted views were manually picked at the central hexameric axis. Manually picked particles were extracted in 4x downsampled 128x128 pixel2 boxes and classified using reference-free 2D classification inside RELION-3.1. Class averages centered at a hexameric axis were used to automatically pick particles inside RELION-3.1. Automatically picked particles were extracted in 4x downsampled 128x128 pixel2 boxes and classified using reference-free 2D classification. Particle coordinates belonging to class averages centered at the hexameric axis were used to train TOPAZ in 5x downsampled micrographs with the neural network architecture conv127. For the final reconstruction, particles were picked using TOPAZ and the previously trained neural network above. Additionally, top, bottom, and side views were picked using the reference-based autopicker inside RELION-3.1, which TOPAZ did not readily identify. Particles were extracted in 4x downsampled 128x128 pixel2 boxes and classified using reference-free 2D classification inside RELION-3.1. Particles belonging to class averages centered at the hexameric axis were combined, and particles within 30 angstrom were removed to prevent duplication after alignment. All resulting particles were then re-extracted in 4x downsampled 128x128 pixel2 boxes.

All side views and a subset of top and bottom views were used for initial model generation in RELION-3.1. The scaled and lowpass filtered output was then used as a starting model for 3D auto refinement in a 512x512 pixel box.

FOURIER SPACE 2.87 OTHER RELION 3.1

Composite map between C2 and C6 symmetrised maps. Created with refmac5 and the reference models as cutoffs

354860 MAXIMUM LIKELIHOOD RELION 3.1

Angle assignment was performed within RELION3.1

MAXIMUM LIKELIHOOD RELION 3.1

Angle assignment was performed within RELION3.1

RELION 3.1 AB INITIO MODEL

Composite map between C2 and C6 created using refmac5

Best Fit RECIPROCAL