2024-05-15 REL PDBe PDBe PDBe 2016-10-21 2016-11-30 2016-11-30 2024-05-15 Biotechnology and Biological Sciences Research Council BB/H005137/1 United Kingdom AICR 11-0261 United Kingdom cryo-electron microscopy reconstruction of microtubule-bound S.pombe kinesin-5 motor domain in the AMPPNP state Goulet A Moores CA microtubule-bound S.pombe kinesin-5, motor domain, AMPPNP bound state, MOTOR PROTEIN Britto M Goulet A Rizvi S von Loeffelholz O Moores CA Cross RA Schizosaccharomyces pombe kinesin-5 switches direction using a steric blocking mechanism. Proc. Natl. Acad. Sci. U.S.A. US 113 E7483 E7489 2016 27834216 doi:10.1073/pnas.1611581113 1091-6490 0040 PNASA6 5m5i FULLOVERLAP 5m5l FULLOVERLAP 5m5m FULLOVERLAP 5m5n FULLOVERLAP 5m5o FULLOVERLAP microtubule-bound S.pombe kinesin-5 motor domain in the AMPPNP state microtubule-bound S.pombe kinesin-5 motor domain in the AMPPNP state 0 1 2 3 0.14 Tubulin alpha-1D chain Bos taurus 0.050107238 1 LEVO MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRT GTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVD YGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA SLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYR GDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYA KRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY Q2HJ86 Tubulin beta-2B chain Bos taurus 0.04990777 1 LEVO MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGP FGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYP DRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGR MSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTG EGMDEMEFTEAESNMNDLVSEYQQYQDATADEQGEFEEEEGEDEA Q6B856 Kinesin-like protein cut7 Schizosaccharomyces pombe (strain 972 / ATCC 24843) 0.040737527 1 Escherichia coli BL21(DE3) LEVO ALHDENETNINVVVRVRGRTDQEVRDNSSLAVSTSGAMGAELAIQSDPSSMLVTKTYAFDKVFGPEADQLMLFENSVAPM LEQVLNGYNCTIFAYGQTGTGKTYTMSGDLSDSDGILSEGAGLIPRALYQLFSSLDNSNQEYAVKCSYYELYNEEIRDLL VSEELRKPARVFEDTSRRGNVVITGIEESYIKNAGDGLRLLREGSHRRQVAATKCNDLSSRSHSIFTITLHRKVSSGMTD ETNSLTINNNSDDLLRASKLHMVDLAGSENIGRSGAENKRARETGMINQSLLTLGRVINALVEKAHHIPYRESKLTRLLQ DSLGGKTKTSMIVTVSSTNTNLEETISTLEYAARAKSIRNKPQNNQLVF P24339 MAGNESIUM ION 2.4305e-05 2 MG GUANOSINE-5'-TRIPHOSPHATE 0.0005231799999999999 1 GTP GUANOSINE-5'-DIPHOSPHATE 0.000443201 1 GDP TAXOL 0.0008539059999999999 1 TA1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER 0.000506196 1 ANP singleParticle helicalArray 6.8 25.0 PIPES 30.0 NaCl 7.0 MgCl2 1.0 EGTA 5.0 AMPPNP C-flat-2/2 COPPER 400 CARBON HOLEY GLOW DISCHARGE ETHANE 100 297 FEI VITROBOT MARK I FEI TECNAI F20 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 70.0 2.0 0.7000000000000001 68000.0 GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER NITROGEN GATAN ULTRASCAN 4000 (4k x 4k) 20.0 1 9.3 FSC 0.5 CUT-OFF FREALIGN 144300 PROJECTION MATCHING SPIDER PROJECTION MATCHING FREALIGN emd_3445.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 50 50 50 55 94 86 50 50 50 110.0 110.0 110.0 90.0 90.0 90.0 X Y Z -5.693818 8.505580999999999 -0.026976306 1.3084207 2.2 2.2 2.2 1.0 AUTHOR Cryo-electron microscopy of microtubule-bound S. pombe kinesin-5 motor domain in the AMPPNP state FLEXIBLE FIT
An initial homology model of S. pombe cut7 kinesin-5 motor domain based on human kinesin-5 structure (PDB 3HQD) was prepared using Modeller. The coordinates of motor bound to an alpha-beta tubulin dimer (PDB 1JFF) were rigidly fitted into the cryo-EM map using Chimera and refined by flexible fitting using Flex-EM. Structural models of loop5 and loop10 were generated using Modeller. The conformation of the neck-linker and the N-terminus were calculated using a conjugate-gradient energy minimization approach.
Cross-correlation coefficient REAL