Cryo-EM structure of RNase P RNA from Geobacillus stearothermophilus, conformer 36

2026-05-13 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY RCSB RCSB 2025-12-03 2026-05-13 2026-05-13 2026-05-13 National Institutes of Health/National Cancer Institute (NIH/NCI) ZIA BC 010379, ZIC BC 011535, ZIA BC 011669 United States Cryo-EM structure of RNase P RNA from Geobacillus stearothermophilus, conformer 36 Degenhardt MFS Stagno J Wang YX RNase P RNA, Geobacillus stearothermophilus, catalytic RNA, cryo-EM structure, conformational heterogeneity, RNA Degenhardt MFS Stagno J Wang YX Cryo-EM structure of RNase P RNA from Geobacillus stearothermophilus, conformer 36 To Be Published 0353 9zhp FULLOVERLAP EMDB EMD-74244 associated EM volume

ribonuclease P RNA ribonuclease P RNA 0 1 Geobacillus stearothermophilus 0.1355 RNase P RNA Geobacillus stearothermophilus 0.13530417199999997 1 GUUAAUCAUGCUCGGGUAAUCGCUGCGGCCGGUUUCGGCCGUAGAGGAAAGUCCAUGCUCGCACGGUGCUGAGAUGCCCG UAGUGUUCGUGCCUAGCGAAUCCAUAAGCUAGGGCAGCCUGGCUUCGGCUGGGCUGACGGCGGGGAAAGAACCUACGUCC GGCUGGGAUAUGGUUCGAUUACCCUGAAAGUGCCACAGUGACGGAGCUCUAAGGGAAACCUUAGAGGUGGAACGCGGUAA ACCCCACGAGCGAGAAACCCAAAUGAUGGUAGGGGCACCUUCCCGAAGGAAAUGAACGGAGGGAAGGACAGGCGGCGCAU GCAGCCUGUAGAUAGAUGAUUACCGCCGGAGUACGAGGCGCAAAGCCGCUUGCAGUACGAAGGUACAGAACAUGGCUUAU AGAGCAUGAUUAACGUC M19021.1 MAGNESIUM ION 2.4305e-05 50 MG water 1.8015e-05 1 HOH singleParticle particle 2.8 7.5 25.0 Tris-HCl buffer 100.0 NaCl Sodium chloride 1.0 MgCl2 Magnesium chloride

25 mM Tris-HCl,pH 7.5, 100 mM NaCl, 1 mM MgCl2

Quantifoil R1.2/1.3 GOLD 300 CARBON HOLEY 200.0 GLOW DISCHARGE 60 AIR 0.02

Glow-discharged Quantifoil R1.2/1.3 Au 300 mesh grids prepared on a Vitrobot. Grids were glow-discharged on both sides for 60 s at 25 mA prior to sample application. Sample concentration was 2.7 mg/mL. A 10 s wait time and 3 s blot with force 3 to 10 at 277K were used during vitrification.

ETHANE 90 277 FEI VITROBOT MARK IV

Grids were glow-discharged on both sides prior to vitrification. Vitrification was performed using a Vitrobot Mark IV with a 10s wait time, followed by a 3s blot and blot force 3 to 10.

The specimen consisted of monomeric RNase P RNA from Geobacillus stearothermophilus purified and prepared in buffer containing 1 mM Magnesium. Samples were applied directly to cryo-EM grids for vitrification

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.5 2.0 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 80.0 100.0 TFS Selectris X 10

The alignment procedure was performed using the EPU software utilizing its autofocus and auto-tuning functions for initial microscope alignment. This was followed by manual fine-tuning adjustments of the beam shift, stigmation, and focus controls to ensure optimal image quality. Grid squares were screened systematically, ensuring the selection of areas with appropriate ice thickness and particle distribution. Image shift calibration and eucentric height adjustment were performed within EPU to maintain beam alignment during data acquisition

FEI FALCON IV (4k x 4k) 4096 4096 5 78777 2.5 53.0 1 21475910

An iterative particle-cleaning workflow was applied, combining 2D classification and heterogeneous refinement with decoy classes to achieve exhaustive particle selection.

PHASE FLIPPING AND AMPLITUDE CORRECTION 9OV3 3.12 FSC 0.143 CUT-OFF cryoSPARC 83114 PROJECTION MATCHING emd_74244.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 351.36 351.36 351.36 90.0 90.0 90.0 X Y Z -0.12416025 0.39258802 -0.00016709974 0.0059601893 0.732 0.732 0.732 0.03 AUTHOR ::::EMDATABANK.org::::EMD-74244:::: 9OV3 A 1-417 PDB experimental model

The initial model consisted of the complete biological assembly

FLEXIBLE FIT maximization of map-to-model correlation REAL 57.0 emd_74244_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 351.36 351.36 351.36 90.0 90.0 90.0 X Y Z -0.39013475 0.611182 0.000094274874 0.03058035 0.732 0.732 0.732 AUTHOR ::::EMDATABANK.org::::EMD-74244:::: emd_74244_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 351.36 351.36 351.36 90.0 90.0 90.0 X Y Z -0.32669306 0.6330177 0.0000911067 0.030974906 0.732 0.732 0.732 AUTHOR ::::EMDATABANK.org::::EMD-74244::::