2024-03-20 REL RCSB RCSB RCSB 2019-04-19 2019-05-01 2019-05-01 2024-03-20 National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB) DP2EB020402 United States National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) NS095892 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI-127533 United States National Institutes of Health/National Institute on Aging (NIH/NIA) AG061697 United States National Institutes of Health/Office of the Director S10OD021634 United States Shin M Asmita A Lon, mitochondrial protease, AAA+, ATPase, HYDROLASE Shin M Puchades C Asmita A Puri N Adjei E Wiseman RL Karzai AW Lander GC Sci Adv US 6 eaba8404 eaba8404 2020 32490208 doi:10.1126/sciadv.aba8404 2375-2548 6on2 FULLOVERLAP Lon protease bound to Y2853 substrate Lon protease bound to Y2853 substrate 0 1 2

Complexes consisting of homohexameric Lon protease from Yersinia pestis bound to Y2853 substrate were isolated using size-exclusion chromatography

Yersinia pestis Cytoplasm ATP-dependent protease La Yersinia pestis 0.057927051 6 Escherichia coli LEVO ALKRKIEAAKMPKDAREKTEAELQKLKMMSPMSAEATVVRGYIDWMLQVPWNSRSKVKKDLVKAQEVLDTDHYGLERVKD RILEYLAVQSRVSKIKGPILCLVGPPGVGKTSLGQSIAKATGRQYVRMALGGVRDEAEIRGHRRTYIGSMPGKLIQKMAK VGVKNPLFLLDQIDKMASDMRGDPASALLEVLDPEQNVAFNDHYLEVDYDLSDVMFVATSNSMNIPAPLLDRMEVIRLSG YTEDEKLNIAKQHLLPKQFERNAIKKGELTIDDSAIMSIIRYYTREAGVRSLEREISKLCRKAVKNLLMDKTVKHIEING DNLKDFLGVQKVDYGRADTENRVGQVTGLAWTEVGGDLLTIETACVPGKGKLTYTGSLGEVMQESIQAALTVVRARADKL GINPDFYEKRDIHVHVPEGATPKDGPSAGIAMCTALVSCLTGNPVRADVAMTGEITLRGLVLPIGGLKEKLLAAHRGGIK VVLIPDDNKRDLEEIPDNVIADLEIHPVKRIDDVLAIALEHPAF A0A3N4AY83 3.4.21.53 Bound Y2853 Substrate Yersinia pestis 0.0005155599999999999

Y2853 substrate was added to Lon and modeled here as a polyalanine chain

1 Escherichia coli LEVO AAAAAAA ADENOSINE-5'-TRIPHOSPHATE 0.000507181 4 ATP MAGNESIUM ION 2.4305e-05 5 MG ADENOSINE-5'-DIPHOSPHATE 0.000427201 2 ADP singleParticle particle 0.95 8.0 50.0 Tris Tris Base 75.0 KCl Potassium Chloride 10.0 MgCl2 Magnesium Chloride 1.0 TCEP TCEP 1.0 ATP Adenosine Triphosphate

Solutions were made fresh from concentrated and filtered using a 0.1 um syringe filter to avoid microbial contamination. Buffers were stored on ice and used within 15 minutes of mixing in order to avoid excess ATP hydrolysis.

Quantifoil, UltrAuFoil, R1.2/1.3 GOLD 300 GLOW DISCHARGE 30 AIR 0.01

Grids were plasma treated for 30 seconds using a 15 mA current operating under atmospheric gases using a glow discharger (Electron Microscopy Sciences).

ETHANE 95 277 HOMEMADE PLUNGER

4 uL of sample was applied per grid and manually blotted for 4 seconds followed by immediately plunge-freezing in liquid ethane cooled by liquid nitrogen..

This sample was monodisperse

FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 70.0 2.7 0.8 0.5 1.2 1.5 36000.0 43478.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 80.0 90.0 0.14

Coma-free alignment procedure from Herzik & Wu, Nature Methods (2017). Preliminary grid screening was performed manually prior to data collection.

GATAN K2 SUMMIT (4k x 4k) COUNTING 3710 3838 0-43 2 4071 11.0 52.0

Images were collected in counting mode at 4 frames per second

1 1176206

template-based cross correlation with FindEM

In silico model was created using ab initio 3D reconstruction using a small subset of the data in cryoSPARC 1 C1 BACK PROJECTION 3.0 FSC 0.143 CUT-OFF RELION 2.0b RELION 2.0b was used to perform final reconstruction

Focused classification of final reconstruction was performed on E and F "step" subunits, resulting in a reconstruction with an overall resolution of 3.5 A by FSC 0.143. The two maps were stitched together using vop max in UCSF Chimera. All three maps (two original and final composite) are deposited in this entry.

118143 MAXIMUM LIKELIHOOD RELION 2.0b RELION 2.0b was used to assign initial euler angles MAXIMUM LIKELIHOOD RELION 2.0b RELION 2.0b was used to assign final euler angles

RELION 2.0b was used to assign initial angles

4 75000.0 RELION 2.0b RELION 2.0b was used to perform final classification

The final 3D classification had a somewhat asymmetric distribution owing to preferred specimen orientation due to interactions with the air-water interface

AB INITIO MODEL

Initial homology model was built using SWISS-MODEL and initial rigid body docking was done using UCSF Chimera

Correlation coefficient REAL 52.0 emd_20133_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 147.2 147.2 147.2 90.0 90.0 90.0 X Y Z -0.032956436 0.08048845 0.0005313212 0.008699856 1.15 1.15 1.15 AUTHOR ::::EMDATABANK.org::::D_1000239684:::: Half-map of E and F subunits used to create composite stitched map for final model building and refinement emd_20133_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 130 130 130 0 0 0 130 130 130 149.5 149.5 149.5 90.0 90.0 90.0 X Y Z -0.030472467 0.07259633 0.00047671382 0.007731027 1.15 1.15 1.15 AUTHOR ::::EMDATABANK.org::::EMD-20133:::: Half-map of E and F subunits used to make composite stitched map for final model building and refinement emd_20133_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 130 130 130 0 0 0 130 130 130 149.5 149.5 149.5 90.0 90.0 90.0 X Y Z -0.13189243 0.24828872 0.0005017059 0.01731279 1.15 1.15 1.15 AUTHOR ::::EMDATABANK.org::::EMD-20133:::: Filtered map of E and F subunits used to make composite stitched map for final model building and refinement emd_20133_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 130 130 130 0 0 0 130 130 130 149.5 149.5 149.5 90.0 90.0 90.0 X Y Z -0.02739812 0.070814885 0.00047669004 0.0077520916 1.15 1.15 1.15 AUTHOR ::::EMDATABANK.org::::EMD-20133:::: Half-map of E and F subunits used to make composite stitched map for final model building and refinement emd_20133_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 147.2 147.2 147.2 90.0 90.0 90.0 X Y Z -0.032956436 0.08048845 0.0005313212 0.008699856 1.15 1.15 1.15 AUTHOR ::::EMDATABANK.org::::D_1000239684:::: Half-map of E and F subunits used to create composite stitched map for final model building and refinement emd_20133_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 130 130 130 0 0 0 130 130 130 149.5 149.5 149.5 90.0 90.0 90.0 X Y Z -0.096705616 0.20978719 0.0005039118 0.016209997 1.15 1.15 1.15 AUTHOR ::::EMDATABANK.org::::EMD-20133:::: Filtered map of A, B, C, and D subunits used to make composite stitched map for final model building and refinement emd_20133_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 130 130 130 0 0 0 130 130 130 149.5 149.5 149.5 90.0 90.0 90.0 X Y Z -0.027749198 0.08155651 0.00047751627 0.00814613 1.15 1.15 1.15 AUTHOR ::::EMDATABANK.org::::EMD-20133:::: Half-map of A, B, C, and D subunits used to make composite stitched map for final model building and refinement emd_20133_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 130 130 130 0 0 0 130 130 130 149.5 149.5 149.5 90.0 90.0 90.0 X Y Z -0.030987103 0.08172838 0.0004787412 0.008139367 1.15 1.15 1.15 AUTHOR ::::EMDATABANK.org::::EMD-20133:::: Half-map of A, B, C, and D subunits used to make composite stitched map for final model building and refinement