6S8M: Kinesin-like protein cut7

S. pombe microtubule decorated with Cut7 motor domain in the AMPPNP state. Determined by electron microscopy at 4.5 Å resolution. Released 21 Aug 2019.

Method: Electron microscopy
Resolution: 4.5 Å
Organism: Schizosaccharomyces pombe
Chains: 3
Atoms: 9,480
Mol. weight: 150.95 kDa
Ligands: GTP, EPB, GDP, ANP
Released: 21 Aug 2019

Explore 6S8M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6S8M contains 55 α-helices and 54 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 22 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	11
β-strand	6-9	4	12
α-helix	10-27	18
β-strand	57-58	2	13
α-helix	65	1
β-strand	66-67	2	13
β-strand	71-73	3	12
α-helix	78-82	5
β-strand	97-98	2	12
α-helix	107	1
α-helix	108-113	6
α-helix	114-119	6
α-helix	123-131	9
β-strand	136	1	11
β-strand	138-142	5	12
β-strand	144	1	14
α-helix	149-165	17
β-strand	169-171	3	12
β-strand	175-176	2	14
α-helix	187-192	6
α-helix	195-200	6
β-strand	208-209	2	14
α-helix	212-218	7
α-helix	228-240	13
α-helix	243-246	4
α-helix	256-262	7
β-strand	273-277	5	15
α-helix	282-285	4
α-helix	292-299	8
α-helix	302-304	3
β-strand	305	1	15
β-strand	316-325	10	15
α-helix	330-340	11
β-strand	347	1	15
β-strand	357-359	3	15
α-helix	363-367	5
β-strand	377-385	9	15
α-helix	389-403	15
α-helix	410-413	4
α-helix	420-439	20

Chain B: 22 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	5
β-strand	7-9	3	6
α-helix	11-28	18
α-helix	42-45	4
β-strand	51-52	2	7
β-strand	60-61	2	7
β-strand	64-67	4	6
α-helix	74	1
α-helix	75-79	5
β-strand	91-92	2	6
α-helix	101-103	3
α-helix	104-108	5
α-helix	109-125	17
β-strand	130-134	5	5
β-strand	138	1	8
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-166	4	5
α-helix	168	1
β-strand	169-170	2	8
α-helix	171-172	2
α-helix	181-194	14
β-strand	198-200	3	5
β-strand	202-203	2	8
α-helix	204-211	8
α-helix	222-236	15
β-strand	244	1	9
α-helix	251-257	7
β-strand	265-266	2	5
β-strand	267-271	5	9
α-helix	286-293	8
α-helix	296-298	3
β-strand	299	1	9
β-strand	310	1	10
β-strand	312-319	8	9
α-helix	323-336	14
β-strand	341	1	10
β-strand	349-354	6	9
β-strand	363-370	8	9
α-helix	374-390	17
α-helix	396-399	4
α-helix	407-419	13
α-helix	422-424	3

Chain K: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	107-111	5	1
α-helix	117-123	7
β-strand	141	1	2
β-strand	149	1	2
β-strand	158-159	2	1
α-helix	165-168	4
α-helix	169-173	5
α-helix	174-181	8
β-strand	186-191	6	1
α-helix	198-202	5
α-helix	219-231	13
β-strand	240-247	8	1
β-strand	252-254	3	1
β-strand	268	1	3
β-strand	278	1	3
β-strand	285-287	3	1
α-helix	290-292	3
α-helix	293-302	10
β-strand	319-326	8	1
β-strand	328	1	4
β-strand	352	1	4
β-strand	356-359	4	1
α-helix	374-395	22
α-helix	410-414	5
β-strand	424-429	6	1
α-helix	446-450	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kinesin-like protein cut7	K	protein	438	Schizosaccharomyces pombe	P24339 (AlphaFold model)
Tubulin beta chain	B	protein	448	Schizosaccharomyces pombe	P05219 (AlphaFold model)
Tubulin alpha-1 chain	A	protein	455	Schizosaccharomyces pombe	P04688 (AlphaFold model)

Sequence of entity 1 (K), FASTA

>6S8M_1 Kinesin-like protein cut7 (chains K)
GIDPFTMAPRVAPGGSQQFLGKQGLKAKNPVSTPNSHFRSASNPRKRREPPTIDTGYPDR
SDTNSPTDHALHDENETNINVVVRVRGRTDQEVRDNSSLAVSTSGAMGAELAIQSDPSSM
LVTKTYAFDKVFGPEADQLMLFENSVAPMLEQVLNGYNCTIFAYGQTGTGKTYTMSGDLS
DSDGILSEGAGLIPRALYQLFSSLDNSNQEYAVKCSYYELYNEEIRDLLVSEELRKPARV
FEDTSRRGNVVITGIEESYIKNAGDGLRLLREGSHRRQVAATKCNDLSSRSHSIFTITLH
RKVSSGMTDETNSLTINNNSDDLLRASKLHMVDLAGSENIGRSGAENKRARETGMINQSL
LTLGRVINALVEKAHHIPYRESKLTRLLQDSLGGKTKTSMIVTVSSTNTNLEETISTLEY
AARAKSIRNKPQNNQLVF

Sequence of entity 2 (B), FASTA

>6S8M_2 Tubulin beta chain (chains B)
MREIVHIQAGQCGNQVGAAFWSTIADEHGLDSAGIYHGTSEAQHERLNVYFNEAAGGKYV
PRAVLVDLEPGTMDAVKSGKFGNLFRPDNIIYGQSGAGNIWAKGHYTEGAELADAVLDVV
RREAEACDALQGFQLTHSLGGGTGSGMGTLLLSKIREEYPDRMMATFSVAPAPKSSDTVV
EPYNATLSMHQLVENSDETFCIDNEALSSIFANTLKIKSPSYDDLNHLVSAVMAGVTTSF
RFPGELNSDLRKLAVNMVPFPRLHFFMVGFAPLAAIGSSSFQAVSVPELTQQMFDANNMM
VAADPRHGRYLTVAALFRGKVSMKEVDEQIRSVQTKNSAYFVEWIPDNVLKAVCSVPPKD
LKMSATFIGNSTSIQEIFRRLGDQFSAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQEAGIDEGDEDYEIEEEKEPLEY

Sequence of entity 3 (A), FASTA

>6S8M_3 Tubulin alpha-1 chain (chains A)
MREVISVHVGQAGVQIGNACWELYCLEHGIGPDGFPTENSEVHKNNSYLNDGFGTFFSET
GQGKFVPRSIYVDLEPNVIDQVRTGPYKDLFHPEQMVTGKEDASNNYARGHYTVGKEMID
SVLERIRRMADNCSGLQGFLVFHSFGGGTGSGLGALLLERLNMEYGKKSNLQFSVYPAPQ
VSTSVVEPYNSVLTTHATLDNSDCTFMVDNEACYDICRRNLDIERPTYENLNRLIAQVVS
SITASLRFAGSLNVDLNEFQTNLVPYPRIHFPLVTYSPIVSAAKAFHESNSVQEITNQCF
EPYNQMVKCDPRTGRYMATCLLYRGDVIPRDVQAAVTSIKSRRTIQFVDWCPTGFKIGIC
YEPPQHVPGSGIAKVNRAVCMLSNTTSIAEAWSRLDHKFDLMYSKRAFVHWYVGEGMEEG
EFSEAREDLAALERDYEEVGQDSMDNEMYEADEEY

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
EPB	7,11-dihydroxy-8,8,10,12,16-pentamethyl-3-[1-methyl-2-(2-methyl-thiazol-4-yl)vi…	C27 H41 N O6 S	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1
MG	Magnesium ion	Mg	1

Primary citation

Cryo-EM Structure (4.5- angstrom ) of Yeast Kinesin-5-Microtubule Complex Reveals a Distinct Binding Footprint and Mechanism of Drug Resistance. von Loeffelholz, O., Pena, A., Drummond, D.R. et al. J Mol Biol (2019) 431:864-872. DOI 10.1016/j.jmb.2019.01.011 · PubMed

Other PDB entries of the same protein (UniProt P24339 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5M5I 9.3 Å, Pseudo-atomic model of microtubule-bound S.pombe kinesin-5 motor domain in the AMPPNP…
5M5L 9.3 Å, Pseudo-atomic model of microtubule-bound S. pombe kinesin-5 motor domain in the AMPPNP…
5M5M 9.3 Å, Pseudo-atomic model of microtubule-bound S.pombe kinesin-5 motor domain in the AMPPNP…
5M5N 9.3 Å, Pseudo-atomic model of microtubule-bound S.pombe kinesin-5 motor domain in the AMPPNP…
5M5O 9.3 Å, Pseudo-atomic model of microtubule-bound S.pombe kinesin-5 motor domain in the AMPPNP…

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