2025-04-09 REL RCSB RCSB RCSB 2023-12-11 2024-09-25 2024-09-25 2025-04-09 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM134867 United States Burman NB Henriques W Wilkinson R Graham A Wiedenheft B Wiedenheft B PARIS, AriA, AriB, DUF4435, IMMUNE SYSTEM Burman N Belukhina S Depardieu F Wilkinson RA Skutel M Santiago-Frangos A Graham AB Livenskyi A Chechenina A Morozova N Zahl T Henriques WS Buyukyoruk M Rouillon C Saudemont B Shyrokova L Kurata T Hauryliuk V Severinov K Groseille J Thierry A Koszul R Tesson F Bernheim A Bikard D Wiedenheft B Isaev A Nature UK 634 424 431 2024 39111359 doi:10.1038/s41586-024-07874-3 1476-4687 0006 NATUAS PARIS immune complex in the assembled state with AriB subunits in a C3-symmetric arrangement. PARIS immune complex in the assembled state with AriB subunits in a C3-symmetric arrangement. 0 1 2 Escherichia coli B185 AriA, ABC ATPase and sensor of PARIS immunity Escherichia coli B185 Escherichia coli BL21(DE3) LEVO MAIRTISKIELSKIHNRYNLTVDFFNDLNVIHGKNGAGKSTLIHVIANIVNGDFIRFAFLIFEEIKATYSDGLKIVIRRDKIDEQSFISVTLSNGKYIKFAVGEAMATVREIESERHLRERDVKSMLAMDIDKFVKENELQKVRASYFPAFRTMLEAWSSSSDVGYERRVIRSSFYNRKASAFARELFGQFLPSINYPSPMEIEDRLREEIRRAQLGIAAYESRTFSESFVKVFSALFDNSSVEGEITGELLKEIEGLAIAQDSSIKNGYYAEYSKVYEEIRSLINRNLKGKVENSVSGALVVYRDALRDRQDYQEKAFSEIDNYMSSVNSFLEDKEMAYDFDLRRKYPKVGLKFPDGSWSPIRVLSSGERQLLTMLYAASKMGDDAIVLIDEPEISLHIDWQEDLLKRMLSQLSGRQIIVCTHSPSIATGYEDFMINISPEFISSRDNDNHKDSEEMEEDESL AriB, DUF4435 and TOPRIM nuclease. Effector of the PARIS immune complex. Escherichia coli B185 Escherichia coli BL21(DE3) LEVO MSSCAYTIDSYITLLTMSSKKRLLVEGRHDRSHLYQLIYKFNPASKVKIDTAQDIKASDKAMSKNNRLKIETIHSKVKGKDNISFLCDREFREFAFNDQIEDLLNSHYCDDSLYWTLGHSLENYFFNPSIIIDAFQFLSPSEYKYKAIELFSELISSSFAVLAAVSLAAKDIDKAGLPAALIDWKDIVINDGTIKLIRRDSYDIDSACVDSFFNAFDAVLPRVIASDVGICSRVVRGHTGILLLQKLFSACLYYVGREDDALQADSSANYFCNLSELSLTTALAESWVRKIGVLEDVYFPDSLLKNIEWSHPQFEK singleParticle particle 7.5 Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY ARRAY GLOW DISCHARGE 45 ETHANE 100 277.15 FEI VITROBOT MARK IV FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.7 0.8 2.5 36000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 1 7340 56.38 1 4078384

Particles Extracted for initial classification Template for particle picking generated from processing a 200 micrograph subset of the data using the blob picker. A volume corresponding to the assembled PARIS complex was identified and Alphafold2 models were docked into the map. ChimeraX's molmap command was used to generate a 20 Angstrom lowpass filtered volume of the docked Alphafold2 models and imported to Cryosparc for template generation.

Multiclass ab-initio reconstructions were used to sort particle images and obtain a consensus refinement.

1 C3 FOURIER SPACE 3.71 FSC 0.143 CUT-OFF cryoSPARC 4.41 Non-Uniform Refinement

cryoSPARC's implementation of Gold-Standard FSC calculation was used.

197018 MAXIMUM LIKELIHOOD cryoSPARC 4.41 Ab-Initio Reconstruction

A three class ab-initio reconstruction was used to remove junk classes.

MAXIMUM LIKELIHOOD cryoSPARC 4.41 Non-Uniform Refinement

After multiple rounds of Ab-initio reconstruction and heterogenous refinement, a 532,010 particle stack was isolated that corresponded to the fully assembled PARIS complex. In this volume, one asymmetric unit of the complex is well-aligned, while in the others, the AriB subunits are present in two, mutually exclusive orientations. This mixture of particles in the assembled PARIS complex correspond to the Cis and Trans arrangements of the complex and as such, the particles were further sorted using focused 3-D classification to isolate the two structural isomers of the complex.

2 211318.0 cryoSPARC 4.41 Focused 3-D Classification

From the 532,010 particle stack identified above, multiple rounds of focused 3-D Classification were used to isolate particle images of the PARIS complex with AriB subunits in the C3 arrangement.

8UX9 PDB experimental model

The initial model consisted of 3 copies of the PDB entry 8UX9

RIGID BODY FIT

Rigid body fitting was done using the fitmap command in ChimeraX to dock 3 copies of the experimentally determined structure of the asymmetric unit into the density map of the fully assembled complex.

Cross-correlation coefficient RECIPROCAL 158.599999999999994 emd_43103_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 331.19998 331.19998 331.19998 90.0 90.0 90.0 X Y Z -0.14264767 0.36738905 0.0003846859 0.013563507 1.104 1.104 1.104 AUTHOR ::::EMDATABANK.org::::EMD-43103:::: Half Map A used for sharpening emd_43103_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 331.19998 331.19998 331.19998 90.0 90.0 90.0 X Y Z -0.11752056 0.40423983 0.00038894566 0.013573859 1.104 1.104 1.104 AUTHOR ::::EMDATABANK.org::::EMD-43103:::: Half Map B used for sharpening