8YY3: Kinesin-14 in nucleotide-free state

Kinesin-14 in nucleotide-free state bound to 14 PF Microtubule. Determined by electron microscopy at 3.24 Å resolution. Released 8 Oct 2025.

Method: Electron microscopy
Resolution: 3.24 Å
Organisms: Sus scrofa, Drosophila melanogaster
Chains: 4
Atoms: 12,668
Mol. weight: 194.24 kDa
Ligands: GTP, GDP, MG, ADP
Released: 8 Oct 2025

Explore 8YY3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YY3 contains 78 α-helices and 70 β-strands across 4 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: 26 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	1
α-helix	10-27	18
α-helix	49-51	3
β-strand	53-55	3	2
β-strand	61-63	3	2
β-strand	65-69	5	1
α-helix	73-80	8
β-strand	93-94	2	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-128	14
β-strand	131-138	8	1
β-strand	140	1	3
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-168	4	1
β-strand	171-172	2	3
α-helix	173-174	2
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-201	2	1
β-strand	203	1	4
β-strand	204-205	2	3
α-helix	206-215	10
α-helix	224-243	20
α-helix	252-259	8
β-strand	269-272	4	4
α-helix	278-281	4
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	4
α-helix	307-309	3
β-strand	312-321	10	4
α-helix	325-337	13
β-strand	343	1	4
β-strand	353	1	4
α-helix	362-363	2
β-strand	373-381	9	4
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-409	5
α-helix	415-436	22

Chain B: 23 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	5
α-helix	10-28	19
β-strand	30	1	6
β-strand	36	1	6
α-helix	41-45	5
α-helix	47-49	3
β-strand	51-54	4	7
β-strand	58-61	4	7
β-strand	63-67	5	5
α-helix	71-78	8
α-helix	87-89	3
β-strand	90-92	3	5
α-helix	101-106	6
α-helix	108-125	18
β-strand	130-136	7	5
α-helix	143-158	16
β-strand	163-167	5	5
β-strand	169	1	8
α-helix	170-172	3
α-helix	181-195	15
β-strand	199-200	2	5
β-strand	202	1	8
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-241	20
β-strand	244	1	9
α-helix	250-257	8
β-strand	265-266	2	5
β-strand	267-270	4	10
α-helix	286-293	8
α-helix	296-298	3
α-helix	305-307	3
β-strand	310-319	10	10
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	10
β-strand	349-351	3	10
β-strand	354	1	9
α-helix	356-358	3
β-strand	363-371	9	10
α-helix	374-387	14
α-helix	395-399	5
α-helix	405-425	21

Chain C: 15 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	297-346	50
β-strand	349-355	7	11
α-helix	356-359	4
α-helix	360-364	5
β-strand	369-371	3	12
β-strand	377-381	5	12
α-helix	385-391	7
β-strand	394-397	4	12
β-strand	400-401	2	11
α-helix	409-423	15
β-strand	427-434	8	11
α-helix	440-444	5
β-strand	446	1	13
β-strand	451	1	13
α-helix	453-468	16
α-helix	469-471	3
β-strand	474-485	12	11
β-strand	488-491	4	11
β-strand	502-504	3	14
β-strand	512-514	3	14
β-strand	520-521	2	11
α-helix	525-538	14
β-strand	554-565	12	11
β-strand	570-580	11	11
α-helix	593-614	22
α-helix	622-624	3
α-helix	626-630	5
α-helix	632-635	4
β-strand	640-647	8	11
α-helix	651-653	3
α-helix	654-669	16

Chain D: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	297-346	50
β-strand	351-355	5	15
α-helix	360-362	3
β-strand	369-373	5	16
β-strand	377-381	5	16
α-helix	385-388	4
β-strand	395-397	3	16
β-strand	400-402	3	15
α-helix	408-423	16
β-strand	428-434	7	15
α-helix	440-444	5
β-strand	446	1	17
β-strand	451	1	17
α-helix	453-468	16
α-helix	469-471	3
β-strand	474-484	11	15
β-strand	489-491	3	15
β-strand	502-504	3	18
β-strand	512-514	3	18
β-strand	520-522	3	15
α-helix	525-538	14
α-helix	550-552	3
β-strand	554-564	11	15
β-strand	575-583	9	15
α-helix	601-614	14
α-helix	622-624	3
α-helix	626-630	5
α-helix	633-635	3
β-strand	640-647	8	15
α-helix	654-670	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A	protein	451	Sus scrofa	Q2XVP4 (AlphaFold model)
Tubulin beta chain	B	protein	444	Sus scrofa	Q767L7 (AlphaFold model)
Protein claret segregational	C, D	protein	409	Drosophila melanogaster	P20480 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8YY3_1 Tubulin alpha-1B chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B), FASTA

>8YY3_2 Tubulin beta chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQVFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMAVTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAEEEEDFGEEAEEEA

Sequence of entity 3 (C, D), FASTA

>8YY3_3 Protein claret segregational (chains C, D)
MHAALSTEVVHLRQRTEELLRCNEQQAAELETCKEQLFQSNMERKELHNTVMDLRGNIRV
FCRIRPPLESEENRMCCTWTYHDESTVELQSIDAQAKSKMGQQIFSFDQVFHPLSSQSDI
FEMVSPLIQSALDGYNICIFAYGQTGSGKTYTMDGVPESVGVIPRTVDLLFDSIRGYRNL
GWEYEIKATFLEIKNEVLYDLLSNEQKDMEIRMAKNNKNDIYVSNITEETVLDPNHLRHL
MHTAKMNRATASTAGNERSSRSHAVTKLELIGRHAEKQEISVGSINLVDLAGSESPKTST
RMTETKNINRSLSELTNVILALLQKQDHIPYRNSKLTHLLMPSLGGNSKTLMFINVSPFQ
DCFQESVKSLRFAASVNSCKMTKAKRNRYLNNSVANSSTQSNNSGNFDK

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
MG	Magnesium ion	Mg	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Primary citation

Structural analysis of a motor with increased mechanical output reveals new transitions in kinesin microtubule motility. Shibata, S., Wang, M.Y., Imasaki, T. et al. Sci Rep (2026) 16:487-487. DOI 10.1038/s41598-025-28573-7 · PubMed

Other PDB entries of the same protein (UniProt Q2XVP4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9U6A 1.92 Å, Tubulin-DARPin D1 in complex with a flavone
5EZY 2.05 Å, Crystal structure of T2R-TTL-taccalonolide AJ complex
5YL2 2.09 Å, Crystal structure of T2R-TTL-Y28 complex
7TTF 2.1 Å, Tubulin-RB3_SLD in complex with compound 12k
5XKG 2.2 Å, Crystal structure of T2R-TTL-CH1 complex
7L05 2.21 Å, Complex of novel maytansinoid M24 bound to T2R-TTL (two tubulin alpha/beta heterodimers,…
9M1M 2.21 Å, Cryo-EM structure of the TBC-DEC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
5JQG 2.24 Å, An apo tubulin-RB-TTL complex structure used for side-by-side comparison
9M1N 2.24 Å, Cryo-EM structure of the TBC-DC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
5XKH 2.25 Å, Crystal structure of T2R-TTL-CF1 complex
7TTD 2.27 Å, Tubulin-RB3_SLD in complex with compound 12e
5JCB 2.3 Å, Microtubule depolymerizing agent podophyllotoxin derivative YJTSF1

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