Pseudo-atomic model of microtubule-bound S.pombe kinesin-5 motor domain in the AMPPNP state (based on cryo-electron microscopy experiment): the N-terminus adopts multiple conformations.

PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

Schizosaccharomyces pombe kinesin-5 switches direction using a steric blocking mechanism.

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.

microtubule-bound S. pombe kinesin-5 motor domain in the AMPPNP state

GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRT
GTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVD
YGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYR
GDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYA
KRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEEGEEY

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGP
FGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYP
DRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGR
MSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTG
EGMDEMEFTEAESNMNDLVSEYQQYQDATADEQGEFEEEEGEDEA

ALHDENETNINVVVRVRGRTDQEVRDNSSLAVSTSGAMGAELAIQSDPSSMLVTKTYAFDKVFGPEADQLMLFENSVAPM
LEQVLNGYNCTIFAYGQTGTGKTYTMSGDLSDSDGILSEGAGLIPRALYQLFSSLDNSNQEYAVKCSYYELYNEEIRDLL
VSEELRKPARVFEDTSRRGNVVITGIEESYIKNAGDGLRLLREGSHRRQVAATKCNDLSSRSHSIFTITLHRKVSSGMTD
ETNSLTINNNSDDLLRASKLHMVDLAGSENIGRSGAENKRARETGMINQSLLTLGRVINALVEKAHHIPYRESKLTRLLQ
DSLGGKTKTSMIVTVSSTNTNLEETISTLEYAARAKSIRNKPQNNQLVF

Schizosaccharomyces pombe (strain 972 / ATCC 24843)

This pseudo-atomic model of S. pombe motor domain shows an alternative conformation of the N-terminus extension.

microtubule-bound S.pombe kinesin-5, motor domain, AMPPNP bound state, MODELLER 9.10 2013-08 complex, motor protein

MRECISVHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRT
GTYRQLFHPEQLITGKEDAANNYARGHYTIGKELIDLVLDRIRKLADQCTGLQGFLIFHSFGGGTGSGFTSLLMERLSVD
YGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYR
GDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYA
KRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGMDSVEGEGEEEEGDEY

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSGP
FGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYP
DRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMMAACDPRHGRYLTVAAIFRGR
MSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTG
EGMDEMEFTEAESNMNDLVSEYQQYQDATADEQGEFEEEEGEDEA

APRVAPGGSQQFLGKQGLKAKNPVSTPNSHFRSASNPRKRREPPTIDTGYPDRSDTNSPTDHALHDENETNINVVVRVRG
RTDQEVRDNSSLAVSTSGAMGAELAIQSDPSSMLVTKTYAFDKVFGPEADQLMLFENSVAPMLEQVLNGYNCTIFAYGQT
GTGKTYTMSGDLSDSDGILSEGAGLIPRALYQLFSSLDNSNQEYAVKCSYYELYNEEIRDLLVSEELRKPARVFEDTSRR
GNVVITGIEESYIKNAGDGLRLLREGSHRRQVAATKCNDLSSRSHSIFTITLHRKVSSGMTDETNSLTINNNSDDLLRAS
KLHMVDLAGSENIGRSGAENKRARETGMINQSLLTLGRVINALVEKAHHIPYRESKLTRLLQDSLGGKTKTSMIVTVSST
NTNLEETISTLEYAARAKSIRNKPQNNQLVFRKVLIKDLVLDI