2024-06-05 REL RCSB RCSB RCSB 2021-08-10 2022-08-17 2022-08-17 2024-06-05 Not funded Cryo-EM structure of Kip3 (AMPPNP) bound to Taxol-Stabilized Microtubules Hernandez-Lopez RA Leschziner AE kinesin-8, microtubules, complex, MOTOR PROTEIN Arellano-Santoyo H Hernandez-Lopez RA Stokasimov E Wang RYR Pellman D Leschziner AE Multimodal tubulin binding by the yeast kinesin-8, Kip3, underlies its motility and depolymerization Biorxiv US 2021 doi:10.1101/2021.10.12.464151 2692-8205 EMD-24667 other EM volume 7rs5 FULLOVERLAP Cryo-EM structure of Kip3 (AMPPNP) bound to Taxol-Stabilized Microtubules Cryo-EM structure of Kip3 (AMPPNP) bound to Taxol-Stabilized Microtubules 0 1 2 3 Taxol-stabilized microtubules 1 1 2 Sus scrofa yeast kinesin-8/ Kip3 1 3 Saccharomyces cerevisiae Tubulin alpha-1A chain Sus scrofa 0.050107238 9 LEVO MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRT GTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVD YGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA SLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYR GDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYA KRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY P02550 Tubulin beta chain Sus scrofa 0.04990777 9 LEVO MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGP FGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYP DRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGR MSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTG EGMDEMEFTEAESNMNDLVSEYQQYQDATADEQGEFEEEGEEDEA P02554 yeast 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 18 MG GUANOSINE-5'-DIPHOSPHATE 0.000443201 9 GDP TAXOL 0.0008539059999999999 9 TA1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER 0.000506196 9 ANP helical helicalArray 8.0
cryoEM buffer (50 mM Tris-HCl, pH 8.0, 1 mM MgCl2, 1 mM EGTA, 1 mM DTT supplemented with 2mM AMPPNP)
 C-flat-1.2/1.3 COPPER GLOW DISCHARGE 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. To prepare Taxol-stabilized microtubules, tubulin was polymerized with a stepwise addition of Taxol as follows: 20 uL of tubulin stock was thawed quickly and placed on ice. 10 uL of BRB80 supplemented with 3 mM GTP were added and the mixture was transferred to a 37 C water bath. After 15, 30, and 45 minutes, additions of 0.5, 0.5, and 1.0 uL of 2 mM Taxol were added by gentle swirling. The mixture was then incubated for an additional 1 h at 37C. 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 2 mM 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 TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 FEI TITAN KRIOS AUTOGRID HOLDER
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 1194 4.0 40.0
Final accumulated electron doses were 40 electrons/A2. Images were collected in super-resolution mode. The total exposure time was 4 seconds, fractionated into 20 subframes, each with an exposure time of 0.2 s.
 1 8.55 -25.76 C14 3.9 FSC 0.143 CUT-OFF FREALIGN
Pseudo-helical symmetry was applied during the reconstruction step
14934 67040 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 emd_24666.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 312.0 312.0 312.0 90.0 90.0 90.0 X Y Z -9.617456000000001 12.935623 0.008799192 0.40784258 1.04 1.04 1.04 0.4 AUTHOR Cryo-EM structure of Kip3 (AMPPNP) bound to taxol-stabilized microtubules 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