9YA5: KIF1A R350G

KIF1A R350G bound to microtubules in two-heads-bound state with AMP-PNP. Determined by electron microscopy at 2.95 Å resolution. Released 22 Apr 2026.

Method: Electron microscopy
Resolution: 2.95 Å
Organisms: Sus scrofa, Homo sapiens
Chains: 6
Atoms: 19,724
Mol. weight: 303.51 kDa
Ligands: GDP, TA1, ANP, MG
Released: 22 Apr 2026

Explore 9YA5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9YA5 contains 132 α-helices and 111 β-strands across 6 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, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	10-28	19
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	132-140	9	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
α-helix	263-265	3
β-strand	269-272	4	1
α-helix	278-281	4
α-helix	288-295	8
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-321	10	1
α-helix	325-336	12
β-strand	343	1	1
β-strand	351-354	4	1
β-strand	355	1	4
α-helix	359-361	3
α-helix	369-370	2
β-strand	373-381	9	1
α-helix	384-399	16
α-helix	405-409	5
α-helix	416-435	20
α-helix	438-439	2

Chain B: 22 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	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	130-138	9	5
α-helix	143-158	16
β-strand	163-170	8	5
α-helix	181-192	12
β-strand	198-203	6	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	310-318	9	8
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	8
β-strand	349-354	6	8
β-strand	364-371	8	8
α-helix	374-389	16
α-helix	396-399	4
α-helix	405-425	21

Chain E: 23 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	9
α-helix	10-28	19
β-strand	35	1	10
α-helix	37-42	6
β-strand	53-55	3	11
β-strand	60	1	10
β-strand	61-63	3	11
β-strand	65-68	4	9
β-strand	69	1	12
α-helix	72-79	8
β-strand	93	1	12
α-helix	103-104	2
α-helix	105-109	5
α-helix	115-128	14
β-strand	134-138	5	9
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	9
α-helix	173-174	2
α-helix	183-194	12
β-strand	200-205	6	9
α-helix	206-215	10
α-helix	224-243	20
β-strand	248	1	13
α-helix	252-259	8
β-strand	269	1	9
β-strand	272	1	9
β-strand	277	1	14
α-helix	278-281	4
α-helix	288-295	8
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-321	10	9
α-helix	325-335	11
β-strand	343	1	9
β-strand	353-354	2	9
β-strand	355	1	13
α-helix	358-361	4
β-strand	368	1	14
β-strand	373-381	9	9
α-helix	384-399	16
α-helix	405-409	5
α-helix	416-435	20
α-helix	438-439	2

Chain I: 27 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	15
α-helix	10-28	19
β-strand	30	1	16
β-strand	36	1	16
α-helix	42-45	4
α-helix	47-49	3
β-strand	51-53	3	17
β-strand	59-61	3	17
β-strand	63-67	5	15
α-helix	70-77	8
α-helix	82-84	3
α-helix	87-89	3
β-strand	90-92	3	15
α-helix	101-102	2
α-helix	103-107	5
α-helix	109-111	3
α-helix	113-126	14
β-strand	132-138	7	15
α-helix	143-158	16
β-strand	163-169	7	15
α-helix	170-172	3
α-helix	181-192	12
β-strand	198-202	5	15
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
α-helix	238-241	4
β-strand	246	1	18
α-helix	250-257	8
β-strand	265-266	2	15
β-strand	267-271	5	18
α-helix	277-280	4
α-helix	286-293	8
α-helix	296-298	3
α-helix	305-307	3
β-strand	310-319	10	18
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	18
β-strand	349-354	6	18
β-strand	363-371	9	18
α-helix	374-389	16
α-helix	395-399	5
α-helix	405-426	22

Chain K: 18 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	19
β-strand	7-12	6	20
α-helix	13-15	3
α-helix	17-21	5
β-strand	26	1	21
β-strand	28-31	4	22
β-strand	34-37	4	22
β-strand	49-51	3	22
β-strand	54-57	4	20
α-helix	70-73	4
α-helix	74-78	5
α-helix	79-87	9
β-strand	91-96	6	20
β-strand	98	1	23
α-helix	103-107	5
α-helix	118-132	15
β-strand	138-149	12	20
β-strand	154-156	3	20
α-helix	160-162	3
β-strand	167-171	5	24
β-strand	175-179	5	24
β-strand	184-185	2	20
α-helix	189-202	14
β-strand	205-206	2	25
β-strand	214-215	2	25
β-strand	218-229	12	20
α-helix	235-236	2
β-strand	240-248	9	20
α-helix	250-251	2
β-strand	252	1	23
α-helix	255-258	4
α-helix	263-290	28
α-helix	310-314	5
α-helix	316-319	4
β-strand	324-331	8	20
β-strand	334	1	21
α-helix	335-337	3
α-helix	338-352	15
β-strand	355	1	19
α-helix	364-378	15

Chain N: 16 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	26
α-helix	17-21	5
β-strand	28-31	4	27
β-strand	34-37	4	27
α-helix	46-47	2
β-strand	48-51	4	27
β-strand	54-56	3	26
α-helix	70-76	7
α-helix	78-86	9
β-strand	90-96	7	26
α-helix	103-107	5
β-strand	109	1	28
β-strand	116	1	28
α-helix	118-133	16
β-strand	138-149	12	26
β-strand	154-156	3	26
α-helix	164-166	3
β-strand	168-170	3	29
β-strand	176-178	3	29
β-strand	184-185	2	26
α-helix	189-202	14
β-strand	205-206	2	30
β-strand	214-215	2	30
β-strand	218-229	12	26
β-strand	238-248	11	26
α-helix	250-252	3
α-helix	263-288	26
α-helix	306-308	3
α-helix	310-314	5
α-helix	316-319	4
β-strand	323-330	8	26
α-helix	338-349	12
α-helix	362-363	2
α-helix	366-378	13

Molecules and chains

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

Sequence of entity 1 (A, E), FASTA

>9YA5_1 Tubulin alpha-1B chain (chains A, E)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, I), FASTA

>9YA5_2 Tubulin beta-2B chain (chains B, I)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (K, N), FASTA

>9YA5_3 Kinesin-like protein KIF1A (chains K, N)
MAGASVKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSYWSHT
SPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMGKQEKDQQGIIP
QLCEDLFSRINDTTNDNMSYSVEVSYMEIYCERVRDLLNPKNKGNLRVREHPLLGPYVED
LSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAETNITTEK
VSKISLVDLAGSERADSTGAKGTRLKEGANINKSLTTLGKVISALAEMDSGPNKNKKKKK
TDFIPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADGAKQIRCNAVI
NEDPNNKLIRELKDEVTRLRDLLYAQGLGDITDGAGVKQLEDKVEELASKNYHLENEVAR
LKKLVEFTSAWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
TA1	Taxol	C47 H51 N O14	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	2
MG	Magnesium ion	Mg	3
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

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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