2025-07-09 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update REFINEMENT_DESCRIPTION chem_comp_atom chem_comp_bond em_3d_fitting_list em_admin pdbx_initial_refinement_model _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_admin.last_update STRUCTURE_SUMMARY em_admin em_software pdbx_entry_details _em_admin.last_update _pdbx_entry_details.has_protein_modification PDBe PDBe 2021-08-11 2021-12-01 2021-12-01 2025-07-09 Wellcome Trust 202231/Z/16/Z United Kingdom Leverhulme Trust Philip Leverhulme Prize United Kingdom von Kugelgen A Bharat TAM S-layer protein RsaA bound to LPS and Holmium, STRUCTURAL PROTEIN Herdman M von Kugelgen A Kureisaite-Ciziene D Duman R El Omari K Garman EF Kjaer A Kolokouris D Lowe J Wagner A Stansfeld PJ Bharat TAM Structure UK 30 215 2022 34800371 doi:10.1016/j.str.2021.10.012 0969-2126 2005 STRUE6 EMD-10389 other EM volume

Specimen with Calcium

7peo FULLOVERLAP Structure of the Caulobacter crescentus S-layer protein RsaA N-terminal domain bound to LPS and soaked with Holmium Structure of the Caulobacter crescentus S-layer protein RsaA N-terminal domain bound to LPS and soaked with Holmium 0 1

Structure of the Caulobacter crescentus S-layer protein RsaA N-terminal domain bound to LPS and soaked with Holmium

Caulobacter vibrioides YB1001 S-layer protein Caulobacter vibrioides YB1001 0.025820353999999997

LPS O-antigen bound to the protein

1 Caulobacter vibrioides CB15 LEVO AYTTAQLVTAYTNANLGKAPDAATTLTLDAYATQTQTGGLSDAAALTNTLKLVNSTTAVAIQTYQFFTGVAPSAAGLDFL VDSTTNTNDLNDAYYSKFAQENRFINFSINLATGAGAGATAFAAAYTGVSYAQTVATAYDKIIGNAVATAAGVDVAAAVA FLSRQANIDYLTAFVRANTPFTAAADIDLAVKAALIGTILNAATVSGIGGYATATAAMINDLSDGALSTDNAAGVNLFTA YPSSGVSGSENLYFQ P35828 CALCIUM ION 4.0078e-05 2 CA HOLMIUM ATOM 0.00016493 1 HO singleParticle particle 2.25 7.5 25.0 C8H18N2O4S HEPES 100.0 NaCl sodium chloride 1.0 MgCl2 magnesium chloride 1.0 CaCl2 calcium chloride 5.0 HoCl3 holmium chloride

Buffer solutions were prepared fresh from sterile filtered concentrated stocksolutions. Solutions were filtered through a 0.22 um filter to avoid microbial contamination and degassed using a vacuum fold pump. The pH of the HEPES stock solution was adjusted with sodium hydroxide at 4 deg C. 5 mM HoCl3 was added to the specimen 1.5 hours before vitrification.

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

20 seconds, 15 mA

ETHANE 100 283.15 FEI VITROBOT MARK IV

Vitrobot options: Blot time 4 seconds, Blot force -13,1, Wait time 10 seconds, Drain time 0.5 seconds,.

RsaA N-terminal domain with LPS soaked with 5 mM HoCl3 for 1.5 h on ice before vitrification

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 -1.0 -1.0 -4.0 -4.0 130000.0 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 70.0 70.0 GIF Quantum LS 20

EPU software

GATAN K2 SUMMIT (4k x 4k) COUNTING 3838 3710 1-20 2 2038 8.0 44.8

Two data collections: First: 0 degree stage tilt with 903 collected movies. Second: 30 degree stage tilt with 1135 collected movies

1

Movies were motion corrected and dose weighted with MotionCor2 (Zheng et al., 2017) implemented in Relion 3.0 (Zivanov et al., 2018). Contrast transfer functions (CTFs) of the resulting motion corrected micrographs were estimated using CTFFIND4 (Rohou and Grigorieff, 2015).

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Initial Particles were extracted in a 2x down-sampled 150 pixel x 150 pixel box and classified using reference-free 2D-classification inside RELION 3.0.

CTFFIND 4.1.13 CTFFIND was used as implemented in Relion 3.0

RELION refinement with in-built CTF correction. The function is similar to a Wiener filter, so amplitude correction included.

PHASE FLIPPING AND AMPLITUDE CORRECTION EMD-10389

30 A lowpass filtered reference map of EMD-10389 was used as starting model.

1 C1 FOURIER SPACE 4.37 FSC 0.143 CUT-OFF RELION 3.0

The final map was obtained from 158,430 particles and post-processed using a soft mask focused on the inner fourteen subunits yielding a resolution of 4.37 A according to the gold standard Fourier shell correlation criterion of 0.143 (Scheres, 2012) with some anisotropy in Z as judged by directional FSCs (Tan et al., 2017)

158430 MAXIMUM LIKELIHOOD RELION 3.0

Angle assignment was performed within RELION 3.0.

MAXIMUM LIKELIHOOD RELION 3.0

Angle assignment was performed within RELION 3.0.

2 RELION 3.0

Particles from classes showing high-resolution features from both datasets were merged, re-extracted in a 300 pixel x 300 pixel box and were subjected to 3D classification using a 30 A lowpass filtered reference map of EMD-10389 (von Kuegelgen et al., 2020).

6T72 A PDB experimental model RIGID BODY FIT

The atomic coordinates (PDB ID 6T72) of our previous cryo-EM structure (von Kugelgen et al., 2020) of the RsaANTD oligomer bound to the O-antigen of lipopolysaccharide (LPS) were rigid body fitted into the final post-processed map from Relion 3.0 (Zivanov et al., 2018) using UCSF Chimera (Pettersen et al., 2004). The resulting fitted model was subjected to real-space refinement using Refmac5 (Murshudov et al., 2011) inside the CCP-EM suite (Burnely et al., 2017), as described previously (von Kugelgen et al., 2020), using reference restraints of the initial structure (PDB ID 6T72) generated with PROSMART (Nicholls et al. 2012).

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