10 Angstrom structure of the asymmetric flagellar filament purified from Leptospira biflexa Patoc WT cells resolved via subtomogram averaging

2024-03-20 REL RCSB RCSB RCSB 2019-07-22 2019-12-25 2020-03-25 2024-03-20 National Institutes of Health/National Library of Medicine (NIH/NLM) R01 GM 110530 United States National Institutes of Health/National Library of Medicine (NIH/NLM) U01 AI088752 United States National Institutes of Health/National Library of Medicine (NIH/NLM) R01 TW009504 United States National Institutes of Health/National Library of Medicine (NIH/NLM) R01 AI052473 United States National Institutes of Health/National Library of Medicine (NIH/NLM) R01 298 AI121207 United States Agencia Nacional de Investigacion e Innovacion (ANII) FCE_3_2016_1_126797 Uruguay Agencia Nacional de Investigacion e Innovacion (ANII) ALI_1_2014_1_4982 Uruguay Agencia Nacional de Investigacion e Innovacion (ANII) FCE_3_2016_1_126797 Uruguay French National Research Agency ANR-18-CE15-0027-1 Uruguay French National Research Agency ANR-08-300 MIE-018 Uruguay 10 Angstrom structure of the asymmetric flagellar filament purified from Leptospira biflexa Patoc WT cells resolved via subtomogram averaging Gibson KH Sindelar CV bacterial flagella, FcpA, FcpB, FlaA, FlaB, Leptospira, STRUCTURAL PROTEIN Gibson KH Trajtenberg F Wunder EA Brady MR San Martin F Mechaly A Shang Z Liu J Picardeau M Ko A Buschiazzo A Sindelar CV An asymmetric sheath controls flagellar supercoiling and motility in the leptospira spirochete. Elife US 9 2020 32157997 doi:10.7554/eLife.53672 2050-084X San Martin F Mechaly AE Larrieux N Wunder EA Ko AI Picardeau M Trajtenberg F Buschiazzo A Crystallization of FcpA from Leptospira, a novel flagellar protein that is essential for pathogenesis. Acta Crystallogr F Struct Biol Commun US 73 123 129 2017 28291747 doi:10.1107/S2053230X17002096 2053-230X ACSFEN Wunder EA Figueira CP Benaroudj N Hu B Tong BA Trajtenberg F Liu J Reis MG Charon NW Buschiazzo A Picardeau M Ko AI A novel flagellar sheath protein, FcpA, determines filament coiling, translational motility and virulence for the Leptospira spirochete. Mol. Microbiol. UK 101 457 470 2016 27113476 doi:10.1111/mmi.13403 1365-2958 2007 MOMIEE Wunder EA Slamti L Suwondo DN Gibson KH Shang Z Sindelar CV Trajtenberg F Buschiazzo A Ko AI Picardeau M FcpB Is a Surface Filament Protein of the Endoflagellum Required for the Motility of the Spirochete Front Cell Infect Microbiol CH 8 130 2018 29868490 doi:10.3389/fcimb.2018.00130 2235-2988 6pwb FULLOVERLAP Flagellar filament purified from the periplasm of the Spirochete bacterium, Leptospira biflexa Flagellar filament purified from the periplasm of the Spirochete bacterium, Leptospira biflexa 0 1 2 3

Filaments were purified from Leptospira biflexa wild type cells.

Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' flagellar filament periplasm Flagellin B1 (FlaB1) Leptospira biflexa serovar Patoc (strain Patoc 1 / ATCC 23582 / Paris) Patoc 1 / ATCC 23582 / Paris bacteria 0.029467032999999997 84 LEVO AAINSHRVLKFQNEEVSKNMEKLSSGMRINRAGDDASGLAVSEKMRTQVNGLRQAERNTEDGMSLIQTTEGFLQESNDII QRIRTLAIQSSNGIYTEEDRQMIQVEVSQLIDEVDRIASQAEFNKMNLLQGDFARGSRATSMWFHIGPNMHQRERVFIAT MTARSLNLKGQSGELLSLSTADKSNDAIGTLDAALTRISKQRANLGAYFNRLEHAAKGLMNAYENTQASESRIRDADMAE ETVAFTKNQILVQSGTAMLAQANVR B0SSZ5 Flagellar coiling protein A (FcpA) Leptospira biflexa serovar Patoc (strain Patoc 1 / ATCC 23582 / Paris) Patoc 1 / ATCC 23582 / Paris bacteria 0.028931002 47 LEVO LTEDQKKKKKEIMEQESLWKNPDFKGYNKTFQELHQLSKTFANNQFRLALSNYQSGVNTIMKNRDWVEQYRKEEAEKKRL DEKWYWQKVDRKAREERVVYREKMKAKQDALNYFSKAINHLDEIKNPDLRERPEFKRLLSDVYRSWIMAEYDLQNLPQTI PILELYIEIDDNEKEYPAHKYLASAYSFEENMIKKTKGPDDMLFKYRYKKNVHLLRATELKYGKDSPEYKHIVNVIN B0STJ8 Flagellar coiling protein B (FcpB) Leptospira biflexa serovar Patoc (strain Patoc 1 / ATCC 23582 / Paris) Patoc 1 / ATCC 23582 / Paris bacteria 0.025539666 32 LEVO SGKSMADTEKELDDNISEVNKRLRLHTVLFKMKVRTLPHKTVLYKGKPSADGERCEAADKQEAQDNTCLHLEVFDFVGSE DGKSSKNLGAKFKKMELFFEGSNNADPDPRKEQPRNLTKIRTYIYQNNFLLEDKVISVIADVAPNGEPAHNDKIELFYQH DDYPVWGTPETPSEKGVGKYILSNVENTKSNPIRNNFKKQFYFKNLDYFDKLFTKIFDYND B0SR03 subtomogramAveraging filament 0.5 6.8

Tris-HCl or ddH20, pH6.8 with <1% sodium azide as a preservative. FIDUCIAL MARKERS: Prior to vitrification, 1 uL of 6x concentrated Gold Tracer beads (10 nm colloidal gold) were mixed with 2 uL of purified flagella. To each grid, 3 uL of this mixture were applied.

Quantifoil R1.2/1.3 COPPER 300 CARBON CONTINUOUS 600.0 PLASMA CLEANING 30 OTHER

Model 950 Solarus Advanced Plasma System manufactured by GATAN.

ETHANE 100 291 FEI VITROBOT MARK III

2 minute incubation time; blot time of 6-7.5 seconds; and blot offset of -2 mm.

Leptospira biflexa serovar Patoc strain Patoc I wild type, fcpA, and fcpB mutant cells cultured in Ellinghausen-McCullough-Johnson-Harris liquid medium until they reached logarithmic phase at 30C. The cells were pelleted and the periplasmic flagellar filaments were purified as described in Wunder et al., 2016; Wunder et al., 2018.

FEI POLARA 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.0 3.0 5.0 15000.0 19230.0 SIDE ENTRY, EUCENTRIC NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 3710 3838 1-12 1 1.2 1.7

Tilt series acquisition. A total of ~35 tilt angles per tilt stack were acquired. The total dose was ~ 60 e/Angstrom2.

Motion correction was performed on movie stacks acquired at each angle in each tilt series using IMOD alignframes. Tilt series were aligned in IMOD eTomo usinf 10 nm fiducial gold markers. CTF estimation with phase flipping was carried out, along with gold bead subtraction in IMOD eTomo. Tilt series were reconstructed using Weighted Back Projection in Tomo3D.

C1 BACK PROJECTION 9.83 FSC 0.143 CUT-OFF emClarity 1.1

emClarity: The two half-dataset volumes were combined with a B-170 factor of 0, and the Gold standard FSC at 0.143 was calculated to be 9.83 A with anisotropic resolutions ranging from 8.89-16.17 Angstrom.

10581 62 15000 de novo Manual selection PEET 1.11 addModPts RELION 2.1 preprocessing.py MODIFIED

Using IMOD 3dmod, filament trajectories were traced by selecting particle points along a single filament. Each continuous filament was a single contour (3dmod). Using the addModPts program in PEET, particle gaps along each filament trajectory contour were filled in with additional points according to a repeat spacing of 52 angstroms. The x,y,z coordinates were then imported into RELION using a modified version of the RELION preprocessing.py python script described in Bharat et. al. (2015). The script was modified to ensure that particles in one filament would be sorted into the same ODD or EVEN grouping to prevent over-estimation of FSC due to inclusion of the 2 or more overlapping particles in a filament in both half-datasets.

MAXIMUM LIKELIHOOD RELION 2.1.b1-gcccuda-2016.10-cc37 3d-autorefinement emClarity 1.0 averaging/alignment

RELION 3d-autorefinment was used to refine angles. In-House particle (x, y, z, and euler angle) coordinate smoothing scripts. emClarity averaging and alignment

emd_20504.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 -96 -96 -96 192 192 192 499.96802 499.96802 499.96802 90.0 90.0 90.0 X Y Z -3.8043377 10.010209 0.15763956 0.89477086 2.604 2.604 2.604 3.15 AUTHOR ::::EMDATABANK.org::::EMD-20504:::: Masked full EM map resulting from subtomogram averaging in emClarity of flagellar filaments purified from wildtype Leptospira biflexa serovar Patoc strain Patoc 1. 5WJT PDB experimental model 6NQW PDB experimental model 6NQZ PDB experimental model RIGID BODY FIT

Eliminate minor clashes between FlaB1, FcpA, and FcpB

Correlation coefficient RECIPROCAL emd_20504_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 -96 -96 -96 192 192 192 499.96802 499.96802 499.96802 90.0 90.0 90.0 X Y Z -4.0974727 9.979717000000001 0.15936355 0.88996357 2.604 2.604 2.604 AUTHOR ::::EMDATABANK.org::::EMD-20504:::: Masked half map 2 resulting from subtomogram averaging in emClarity of flagellar filaments purified from wildtype Leptospira biflexa serovar Patoc strain Patoc 1. emd_20504_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 -96 -96 -96 192 192 192 499.96802 499.96802 499.96802 90.0 90.0 90.0 X Y Z -7.696319 10.177825 -0.008705929 1.3833222 2.604 2.604 2.604 AUTHOR ::::EMDATABANK.org::::EMD-20504:::: Unmasked full EM map resulting from subtomogram averaging in emClarity of flagellar filaments purified from wildtype Leptospira biflexa serovar Patoc strain Patoc 1. emd_20504_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 -96 -96 -96 192 192 192 499.96802 499.96802 499.96802 90.0 90.0 90.0 X Y Z -11.228661000000001 57.538753999999997 1.733903 6.6346426 2.604 2.604 2.604 AUTHOR ::::EMDATABANK.org::::EMD-20504:::: Symmetrised map generated by rotational symmetrization of the L. biflexa Patoc WT filament core resulting from subtomogram averaging. Map used to calculate helical parameters for FlaB core model. emd_20504_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 -96 -96 -96 192 192 192 499.96802 499.96802 499.96802 90.0 90.0 90.0 X Y Z -3.860492 10.420686 0.15210588 0.8619554 2.604 2.604 2.604 AUTHOR ::::EMDATABANK.org::::EMD-20504:::: Masked half map 1 resulting from subtomogram averaging in emClarity of flagellar filaments purified from wildtype Leptospira biflexa serovar Patoc strain Patoc 1. emd_20504_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 -96 -96 -96 192 192 192 499.96802 499.96802 499.96802 90.0 90.0 90.0 X Y Z -8.629213 10.391157 -0.0050514303 1.3821759 2.604 2.604 2.604 AUTHOR ::::EMDATABANK.org::::EMD-20504:::: Unmasked-half map 2 resulting from subtomogram averaging in emClarity of flagellar filaments purified from wildtype Leptospira biflexa serovar Patoc strain Patoc 1. emd_20504_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 -96 -96 -96 192 192 192 499.96802 499.96802 499.96802 90.0 90.0 90.0 X Y Z -7.010304 9.997104999999999 -0.012112087 1.3833374 2.604 2.604 2.604 AUTHOR ::::EMDATABANK.org::::EMD-20504:::: Unmasked-half map 1 resulting from subtomogram averaging in emClarity of flagellar filaments purified from wildtype Leptospira biflexa serovar Patoc strain Patoc 1.