2024-02-28 REL RCSB RCSB RCSB 2021-08-11 2022-08-17 2022-08-17 2024-02-28 Not funded Hernandez-Lopez RA Leschziner AE kinesin-8, microtubules, complex, MOTOR PROTEIN Arellano-Santoyo H Hernandez-Lopez RA Stokasimov E Wang RY-R Pellman D Lesczhiner AE Biorxiv US 2024 doi:10.1101/2021.10.12.464151 2692-8205 EMD-24666 other EM volume 7rs6 FULLOVERLAP Cryo-EM structure of Kip3 (AMPPNP) bound to GMPCPP-Stabilized Microtubules Cryo-EM structure of Kip3 (AMPPNP) bound to GMPCPP-Stabilized Microtubules 0 1 2 3 GMPCPP-stabilized microtubules 1 1 2 Sus scrofa yeast kinesin-8/ Kip3 1 3 Saccharomyces cerevisiae Tubulin alpha-1B chain Sus scrofa 0.050204445 9 LEVO MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRT GTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVD YGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYR GDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYA KRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY Q2XVP4 Tubulin beta chain Sus scrofa 0.04990777 9 LEVO MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGP FGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYP DRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGR MSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTG EGMDEMEFTEAESNMNDLVSEYQQYQDATADEQGEFEEEGEEDEA P02554 kinesin-8/ Kip3 Saccharomyces cerevisiae 0.039900332000000004 9 Saccharomyces cerevisiae LEVO MNVPETRQSSIVVAIRVRPFTSMEKTRLVIRKIVDCVDDRMLIFDPADRNSNATNKFSSQRRRHGGEIKFVFDKLFDETS SQARVYKETTSPLLDSVLDGFNSTVFAYGATGCGKTYTVSGTPSQPGIIFLAMEELFNKITDLKDEKDFEISLSYLEIYN ERIRDLLKPETPSKRLVIREDTQNHIKVANLSYHHPNTVEDVMDLVVQGNINRTTSPTEANEVSSRSHAVLQIHIMQTNK LVDLTSQHTFATLSIIDLAGSERAAATRNRGIRLHEGANINRSLLALGNCINALCLNDGSRSCHIPYRDSKLTRLLKFSL GGNCKTVMIVCISPSSSHYDETLNTLKYANRAKEI GUANOSINE-5'-TRIPHOSPHATE 0.0005231799999999999 9 GTP MAGNESIUM ION 2.4305e-05 27 MG PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER 0.0005212079999999999 9 G2P PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER 0.000506196 9 ANP helical helicalArray 6.8

BRB80 buffer (80 mM PIPES-KOH, pH 6.8; 1 mM MgCl2, 1 mM EGTA, 1 mM DTT)

ETHANE 100 22 FEI VITROBOT MARK IV

Highly purified, glycerol-free tubulin (Cytoskeleton, Inc.) was resuspended in BRB80 buffer (80 mM PIPES-KOH, pH 6.8, 1 mM MgCl2, 1 mM EGTA, 1 mM DTT) to a concentration of 10 mg/mL. GMPCPP microtubules were polymerized using GMPCPP seeds (20 uM tubulin, 1mM GMPCPP, 1mM MgCl2, 1mM DTT in BRB80). A 1 uL aliquot of seeds was transferred to a 37 C water bath. After 30 minutes, 40 uL of elongation mix (2 uM tubulin, 0.5 mM GMPCPP, 0.5 mM MgCl2, 1 mM DTT in BRB80) were added and the mixture was then incubated for additional 4.5 - 5 hours at 37 C. Purified Kip3 438 protein was buffer exchanged to cryoEM buffer (50 mM Tris-HCl, pH 8.0, 1 mM MgCl2, 1 mM EGTA, 1 mM DTT supplemented with 2mM AMPPNP) and desalted using a ZEBA spin desalting column. The protein was recovered by centrifugation at 15,000 rcf for 2 min. A final spin at 30,000 x g in a TLA 100 rotor (Beckman) for 10 min at 4 C was carried out to remove big aggregates.

FEI POLARA 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300

Images were recorded using a semi-automated acquisition program Serial EM with a defocus range from 1.5 to 3.5 um.

GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 1 643 5.0 40.0

Final accumulated electron doses were 40 electrons/A2. Images were collected in super-resolution mode. The total exposure time was 5 seconds, fractionated into 20 subframes, each with an exposure time of 0.25 s.

1 8.9 -25.76 C14 BACK PROJECTION 4.1 FSC 0.143 CUT-OFF FREALIGN 21788 29090 Appion

Inspection, defocus estimation, microtubule picking, and stack creation were performed within the Appion processing environment (Lander et al., 2009). Images were selected for processing on the basis of high decoration, straight MTs, and the absence of crystalline ice.

NOT APPLICABLE FREALIGN 3JAT A PDB experimental model 3JAT B PDB experimental model 4FRZ K PDB experimental model OTHER

Multiple rounds of refinement were carried out against one half map (training map), and the other half map (validation map) was used to monitor overfitting based on the procedure described in Wang et al. elife, 2016. It is to note that the molecular interactions of ligand-protein were restrained to the initial poses adapted from the high-resolution structures during structure refinement.

Overall correlation of the residues to the map REAL 100.0