2024-10-23 REL RCSB RCSB RCSB 2021-04-18 2021-06-02 2021-06-02 2024-10-23 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI034036 United States Wang X Brown A Sibley LD Zhang R cortical, parasite, STRUCTURAL PROTEIN Wang X Fu Y Beatty WL Ma M Brown A David Sibley L Zhang R Nat Commun UK 12 3065 3065 2021 34031406 doi:10.1038/s41467-021-23351-1 2041-1723 EMD-23870 other EM volume 7miz FULLOVERLAP cortical microtubule with associated MIPs cortical microtubule with associated MIPs 0 1 2 3 4 5 Toxoplasma gondii Microtubule associated protein SPM1 Toxoplasma gondii 0.03884575 24 LEVO MSGGNSNTPKKLPSEEGSDYGYPQKPQKYLPKSEQAEPDYSACCKGNDAYKGASHGTVQFSHPEEAQKYAGAAAGAETIQ RGRERVAADRQPRAAGDVPARRLHLSDVDEAHRGQSPSRHPGYCVEELCTCGMHKCIPSRAPVPFTGSTQYRQEFVPKPL PPPTQVSQVTLPPSLPFEAESSYRTEFVAKPLPPPAKFSEVKLPPTLPFHGESAYRTDYVPKPLPEVAKPVEVKLPPTLP FNAQSCYRSEYVAKPLPPPVQTVEVKLPPSLPFEGSTHYRDEFQVKPLPPATKVTEVKLPPSLPFDATSMYRSDYVAKSN PICPVSKLPQYPAATYPQNHVFWDPDTKQWY A0A7J6K285 Tubulin alpha chain Toxoplasma gondii 0.050166644999999996 26 LEVO MREVISIHVGQAGIQIGNACWELFCLEHGIQPDGQMPSDKTIGGGDDAFNTFFSETGAGKHVPRCVFLDLEPTVVDEVRT GTYRHLFHPEQLISGKEDAANNFARGHYTIGKEIVDLSLDRIRKLADNCTGLQGFLMFNAVGGGTGSGLGCLLLERLSVD YGKKSKLNFCSWPSPQVSTAVVEPYNSVLSTHSLLEHTDVAVMLDNEAIYDICRRNLDIERPTYTNLNRLIAQVISSLTA SLRFDGALNVDVTEFQTNLVPYPRIHFMLSSYAPIISAEKAYHEQLSVAEITNSAFEPASMMAKCDPRHGKYMACCLMYR GDVVPKDVNAAVATIKTKRTIQFVDWCPTGFKCGINYQPPTVVPGGDLAKVMRAVCMISNSTAIAEVFSRMDHKFDLMYA KRAFVHWYVGEGMEEGEFSEAREDLAALEKDYEEVGIETAEGEGEEEGYGDEY P10873 Tubulin beta chain Toxoplasma gondii 0.050119120999999996 26 LEVO MREIVHVQGGQCGNQIGAKFWEVISDEHGIDPTGTYCGDSDLQLERINVFYNEATGGRFVPRAILMDLEPGTMDSVRAGP FGQLFRPDNFVFGQTGAGNNWAKGHYTEGAELIDSVLDVVRKEAEGCDCLQGFQITHSLGGGTGSGMGTLLISKVREEYP DRIMETFSVFPSPKVSDTVVEPYNATLSVHQLVENADEVQVIDNEALYDICFRTLKLTTPTYGDLNHLVSAAMSGVTCCL RFPGQLNSDLRKLAVNLIPFPRLHFFLIGFAPLTSRGSQQYRALSVPELTQQMFDAKNMMCASDPRHGRYLTASAMFRGR MSTKEVDEQMLNVQNKNSSYFVEWIPNNMKSSVCDIPPKGLKMSVTFVGNSTAIQEMFKRVSDQFTAMFRRKAFLHWYTG EGMDEMEFTEAESNMNDLVSEYQQYQDATAEEEGEFDEEEGEMGAEEGA I7BFC9 PDI family protein Toxoplasma gondii 0.024939331999999998 20 LEVO MSQPVFASPLNVEKRRLNEERALMQAQKAGGEGVNIQLPPNYGDMDLILFPEGSLKNSNNTVIPQSHLKGKSVALYFADG ADPKCASLLPFLLNYYRTMNEGGANQKIEIIFVSLDRDREAFESHRAHMPWLSIDLENPLTEILKRHFRVMKEYEVPTYG YGSRTGVPSVIVIGSDGREAQFLPICSGLEEGDRALLRWDWRNTKFASDQFHVRPTLLEQ Q8MPF4 PDI family protein Toxoplasma gondii 0.021687934 4 LEVO MLAADCFFGPDVVKRTQQGNYVPVRPDHFAGVSVALFFAKAGHSKCAQIVPVVRQFYKTTNFSGEKAVIEIIYVSLDKDE QDFERVRALMPWCSVEYKSCLRKKLIERYRVPNGELAFGTVRIPSTAIPLLIVIGPNGEEAGRMNFQQSDEFVLQRWDYR FNKWPGSAQRLRTLNDATDPWKKRLPQNV A0A7J6K232 GUANOSINE-5'-TRIPHOSPHATE 0.0005231799999999999 26 GTP MAGNESIUM ION 2.4305e-05 26 MG GUANOSINE-5'-DIPHOSPHATE 0.000443201 26 GDP singleParticle filament 7.4 Quantifoil R2/2 COPPER 300 GLOW DISCHARGE 50 AIR ETHANE 95 289 FEI VITROBOT MARK IV

blot for 4 seconds with a blot force of -15.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.01 1.0 3.5 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 BIOQUANTUM (6k x 4k) 3838 3710 2 9231 9.0 63.7

Images were collected in counting mode, with an exposure rate of 8.5 electrons/pixel/s on the detector camera.

1 536132

Cortical MTs were manually picked from the motion-corrected micrographs using the APPION image-processing suite. The selected MT segments were computationally cut into overlapping boxes (512x512 pixels) with an 8-nm non-overlapping region (step size) between adjacent boxes (corresponding to the length of a tubulin heterodimer). We refer to these boxed images as 8-nm MT particles.

We used 13- and 14-protofilament bovine GMPCPP-MTs as the initial models, and performed multi-reference sorting of all the 8-nm MT particles using EMAN1.

C1 FOURIER SPACE 3.4 FSC 0.143 CUT-OFF RELION 3.1 cryoSPARC 2.15 220139 PROJECTION MATCHING 300 3.0 EMAN 1.9

The classification result indicated that T. Gondii cortical MTs are exclusively 13-protofilament MTs.

MAXIMUM LIKELIHOOD RELION 3.1

Next, we performed single-reference refinement using Refine3D in RELION-3 software with global search of alignment parameters. The structure gradually converged to a 13-protofilament MT with 3-start helix and only one seam.

2 RELION 3.1

To separate the particles with and without TrxL2, we signal-subtracted the tubulin densities from the raw particle images using Particle subtraction in RELION-3, and then performed 3D classification with a soft-edged cylindrical mask covering only the TrxL2 densities at either site x or y. For each site, the 3D classification was able to produce two clean classes, corresponding to the bound and unbound states of TrxL2.

4FYU PDB experimental model 6U42 PDB experimental model 3JAS PDB experimental model AB INITIO MODEL

Secondary structure, Ramachandran, and rotamer restraints were applied during refinement. The nonbonded_weight value was set to 500 to reduce the clashes between atoms.

emd_23869_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 438.4 438.4 438.4 90.0 90.0 90.0 X Y Z -0.6182673 2.0005019 0.022630855 0.0996883 1.096 1.096 1.096 AUTHOR ::::EMDATABANK.org::::EMD-23869:::: B-factor sharpened composite map of T. gondii cortical microtubule (with TrxL2) emd_23869_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 438.4 438.4 438.4 90.0 90.0 90.0 X Y Z 0.0 1.1932566 0.022630854 0.07987491 1.096 1.096 1.096 AUTHOR ::::EMDATABANK.org::::EMD-23869:::: Unsharpened composite map of T. gondii cortical microtubule (with TrxL2)