9YAB: KIF1A R350W

KIF1A R350W bound to microtubules in the apo state. Determined by electron microscopy at 3.21 Å resolution. Released 22 Apr 2026.

Method: Electron microscopy
Resolution: 3.21 Å
Organisms: Sus scrofa, Homo sapiens
Chains: 3
Atoms: 9,687
Mol. weight: 151.37 kDa
Ligands: TA1, GDP, MG, GTP
Released: 22 Apr 2026

Explore 9YAB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9YAB contains 65 α-helices and 53 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: 24 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	10-27	18
α-helix	37-42	6
β-strand	53-55	3	2
β-strand	61-63	3	2
β-strand	65-68	4	1
β-strand	69	1	3
α-helix	72-79	8
β-strand	93	1	3
α-helix	103-104	2
α-helix	105-109	5
α-helix	115-128	14
β-strand	132-138	7	1
α-helix	144-160	17
β-strand	165-172	8	1
α-helix	173-174	2
α-helix	183-189	7
α-helix	191-192	2
α-helix	193-197	5
β-strand	200-205	6	1
α-helix	206-215	10
α-helix	224-243	20
β-strand	248	1	4
α-helix	252-259	8
β-strand	269-272	4	4
α-helix	278-281	4
α-helix	288-293	6
α-helix	294-296	3
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-321	10	4
α-helix	325-336	12
β-strand	343	1	4
β-strand	351-356	6	4
β-strand	373-381	9	4
α-helix	384-399	16
α-helix	405-409	5
α-helix	415-435	21
α-helix	438-439	2

Chain B: 24 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	5
α-helix	10-28	19
β-strand	30	1	6
β-strand	36	1	6
α-helix	42-45	4
α-helix	47-49	3
β-strand	51-53	3	7
β-strand	59-61	3	7
β-strand	63-67	5	5
α-helix	71-77	7
α-helix	87-89	3
β-strand	90-92	3	5
α-helix	101-102	2
α-helix	103-107	5
α-helix	109-126	18
β-strand	129-138	10	5
α-helix	143	1
α-helix	144-148	5
α-helix	149-158	10
β-strand	163-169	7	5
α-helix	181-195	15
β-strand	198-202	5	5
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
β-strand	246	1	8
α-helix	250-257	8
β-strand	265-266	2	5
β-strand	267-271	5	8
α-helix	286-294	9
α-helix	296-298	3
α-helix	305-307	3
β-strand	310-319	10	8
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	8
β-strand	349-354	6	8
β-strand	363-371	9	8
α-helix	374-389	16
α-helix	396-399	4
α-helix	405-424	20

Chain K: 17 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	9
α-helix	13-15	3
α-helix	17-21	5
β-strand	28-31	4	10
β-strand	34-37	4	10
α-helix	46-47	2
β-strand	48-51	4	10
β-strand	54-57	4	9
β-strand	67	1	9
α-helix	70-73	4
α-helix	74-78	5
α-helix	79-87	9
β-strand	91-96	6	9
α-helix	103-107	5
β-strand	109	1	11
β-strand	116	1	11
α-helix	118-133	16
β-strand	135	1	9
β-strand	138-150	13	9
β-strand	153-156	4	9
α-helix	164-165	2
β-strand	166	1	9
α-helix	167	1
β-strand	168-171	4	12
β-strand	175-178	4	12
β-strand	184-186	3	9
α-helix	189-202	14
β-strand	205-206	2	13
β-strand	214-215	2	13
β-strand	218-230	13	9
β-strand	236-248	13	9
α-helix	249-252	4
α-helix	263-289	27
α-helix	299-301	3
α-helix	310-314	5
α-helix	316-319	4
β-strand	324-331	8	9
α-helix	338-350	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A	protein	451	Sus scrofa	Q2XVP4 (AlphaFold model)
Tubulin beta-2B chain	B	protein	445	Sus scrofa	A0A8D1UIR5 (AlphaFold model)
Kinesin-like protein KIF1A	K	protein	438	Homo sapiens	Q12756 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9YAB_1 Tubulin alpha-1B chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B), FASTA

>9YAB_2 Tubulin beta-2B chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (K), FASTA

>9YAB_3 Kinesin-like protein KIF1A (chains K)
MAGASVKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSYWSHT
SPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMGKQEKDQQGIIP
QLCEDLFSRINDTTNDNMSYSVEVSYMEIYCERVRDLLNPKNKGNLRVREHPLLGPYVED
LSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAETNITTEK
VSKISLVDLAGSERADSTGAKGTRLKEGANINKSLTTLGKVISALAEMDSGPNKNKKKKK
TDFIPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADWAKQIRCNAVI
NEDPNNKLIRELKDEVTRLRDLLYAQGLGDITDGAGVKQLEDKVEELASKNYHLENEVAR
LKKLVEFTSAWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
TA1	Taxol	C47 H51 N O14	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
MG	Magnesium ion	Mg	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1

Primary citation

Pathogenic KIF1A R350 mutations disrupt a conserved and conformation-dependent kinesin-tubulin salt bridge. Shatarupa, A., Rao, L., Asenjo, A.B. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-71026-6 · 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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