8UTY: Tubulin alpha-1B chain

KIF1A[1-393] P364L mutant AMP-PNP bound two-heads-bound state in complex with a microtubule. Determined by electron microscopy at 3.3 Å resolution. Released 12 Jun 2024.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Sus scrofa, Homo sapiens
Chains: 7
Atoms: 23,765
Mol. weight: 354.5 kDa
Ligands: GTP, MG, ANP, TA1
Released: 12 Jun 2024

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

Secondary structure: helices and β-sheets

8UTY contains 159 α-helices and 128 β-strands across 7 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, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	10-28	19
β-strand	35	1	2
α-helix	37-42	6
β-strand	53-55	3	3
β-strand	60	1	2
β-strand	61-63	3	3
β-strand	65-68	4	1
β-strand	69	1	4
α-helix	72-79	8
α-helix	82-85	4
β-strand	93	1	4
α-helix	103-104	2
α-helix	105-109	5
α-helix	114-128	15
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	224-239	16
α-helix	240-242	3
β-strand	248	1	5
α-helix	252-257	6
β-strand	269-272	4	5
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	5
α-helix	325-337	13
β-strand	343	1	5
β-strand	351-356	6	5
α-helix	359-361	3
α-helix	369-370	2
β-strand	373-381	9	5
α-helix	384-399	16
α-helix	405-409	5
α-helix	416-436	21

Chain B: 25 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	6
α-helix	10-28	19
β-strand	30	1	7
β-strand	36	1	7
α-helix	41-43	3
α-helix	47-49	3
β-strand	51-53	3	8
β-strand	59-61	3	8
β-strand	63-67	5	6
α-helix	70-77	8
α-helix	87-89	3
β-strand	90-92	3	6
α-helix	101-102	2
α-helix	103-107	5
α-helix	109-125	17
β-strand	130-138	9	6
α-helix	143-158	16
β-strand	163-170	8	6
α-helix	181-194	14
β-strand	199-203	5	6
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
α-helix	238-241	4
β-strand	246	1	9
α-helix	250-257	8
β-strand	265-266	2	6
β-strand	267-271	5	9
α-helix	283-284	2
α-helix	286-294	9
α-helix	296-298	3
α-helix	305-307	3
β-strand	310-318	9	9
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	9
β-strand	349-354	6	9
β-strand	364-371	8	9
α-helix	372-374	3
α-helix	375-389	15
α-helix	396-399	4
α-helix	405-423	19

Chain E: 25 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	10
α-helix	10-28	19
α-helix	37-42	6
β-strand	53-55	3	11
β-strand	61-63	3	11
β-strand	65-68	4	10
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	132-138	7	10
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	10
α-helix	173-174	2
α-helix	183-189	7
α-helix	191-196	6
β-strand	200-205	6	10
α-helix	206-215	10
α-helix	224-239	16
α-helix	240-242	3
β-strand	248	1	13
α-helix	252-259	8
β-strand	269-272	4	13
α-helix	278-281	4
α-helix	288-295	8
α-helix	307-309	3
β-strand	312-321	10	13
α-helix	325-336	12
β-strand	343	1	13
β-strand	352-356	5	13
α-helix	358-361	4
α-helix	368-370	3
β-strand	373-381	9	13
α-helix	384-399	16
α-helix	405-409	5
α-helix	415-435	21
α-helix	438	1

Chain I: 26 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	14
α-helix	10-28	19
β-strand	30	1	15
β-strand	36	1	15
α-helix	41-44	4
α-helix	47-49	3
β-strand	51-53	3	16
β-strand	59-61	3	16
β-strand	63-67	5	14
α-helix	70-77	8
α-helix	82-84	3
α-helix	87-89	3
β-strand	90-92	3	14
α-helix	101-102	2
α-helix	103-107	5
α-helix	109-125	17
β-strand	129-138	10	14
α-helix	143-158	16
β-strand	163-170	8	14
α-helix	181-194	14
β-strand	198-203	6	14
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
α-helix	238-241	4
β-strand	246	1	17
α-helix	250-257	8
β-strand	265-266	2	14
β-strand	267-271	5	17
α-helix	276-281	6
α-helix	286-294	9
α-helix	296-298	3
α-helix	305-307	3
β-strand	310-319	10	17
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	17
β-strand	349-354	6	17
β-strand	363-371	9	17
α-helix	372-374	3
α-helix	375-389	15
α-helix	396-399	4
α-helix	405-423	19

Chain K: 16 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	18
α-helix	6	1
β-strand	7-12	6	19
α-helix	17-21	5
β-strand	26	1	20
β-strand	28-31	4	21
β-strand	34-37	4	21
β-strand	49-51	3	21
β-strand	54-57	4	19
β-strand	67	1	19
α-helix	70-73	4
α-helix	74-78	5
α-helix	79-87	9
β-strand	91-97	7	19
β-strand	98	1	22
α-helix	103-107	5
β-strand	109	1	23
β-strand	116	1	23
α-helix	118-132	15
β-strand	138-149	12	19
β-strand	154-156	3	19
β-strand	166	1	19
β-strand	168-171	4	24
β-strand	175-178	4	24
β-strand	184-185	2	19
α-helix	189-202	14
β-strand	205-206	2	25
β-strand	214-215	2	25
β-strand	218-229	12	19
β-strand	240-248	9	19
α-helix	249-251	3
β-strand	252	1	22
α-helix	255-258	4
α-helix	263-295	33
α-helix	310-314	5
α-helix	316-319	4
β-strand	324-331	8	19
β-strand	334	1	20
α-helix	335-337	3
α-helix	338-352	15
β-strand	355	1	18
α-helix	364-385	22

Chain N: 17 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	30
α-helix	17-21	5
α-helix	24-25	2
β-strand	26	1	31
β-strand	28-31	4	32
β-strand	34-37	4	32
β-strand	48-51	4	32
β-strand	54-57	4	30
α-helix	70-73	4
α-helix	74-78	5
α-helix	79-86	8
β-strand	91-96	6	30
α-helix	103-108	6
β-strand	109	1	33
β-strand	116	1	33
α-helix	118-133	16
β-strand	138-150	13	30
β-strand	153-156	4	30
α-helix	165	1
β-strand	166	1	30
α-helix	167	1
β-strand	168-171	4	34
β-strand	175-178	4	34
β-strand	184-185	2	30
α-helix	189-201	13
β-strand	205-206	2	35
β-strand	214-215	2	35
β-strand	218-230	13	30
β-strand	236-247	12	30
α-helix	250-252	3
α-helix	263-294	32
α-helix	310-314	5
α-helix	316-319	4
β-strand	324-331	8	30
β-strand	334	1	31
α-helix	335-337	3
α-helix	338-348	11
α-helix	364-386	23

Chain S: 24 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	26
α-helix	10-28	19
α-helix	37-42	6
β-strand	53-55	3	27
β-strand	61-63	3	27
β-strand	65-68	4	26
β-strand	69	1	28
α-helix	73-79	7
β-strand	93	1	28
α-helix	103-104	2
α-helix	105-109	5
α-helix	115-128	14
β-strand	132-140	9	26
α-helix	145-160	16
β-strand	165-172	8	26
α-helix	173-174	2
α-helix	183-189	7
α-helix	191-196	6
β-strand	200-205	6	26
α-helix	206-215	10
α-helix	224-239	16
α-helix	240-242	3
β-strand	248	1	29
α-helix	252-259	8
β-strand	269-272	4	29
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	29
α-helix	325-337	13
β-strand	343	1	29
β-strand	352-356	5	29
α-helix	359-361	3
α-helix	368-370	3
β-strand	373-381	9	29
α-helix	384-399	16
α-helix	406-411	6
α-helix	415-436	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A, E, S	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, S), FASTA

>8UTY_1 Tubulin alpha-1B chain (chains A, E, S)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, I), FASTA

>8UTY_2 Tubulin beta-2B chain (chains B, I)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (K, N), FASTA

>8UTY_3 Kinesin-like protein KIF1A (chains K, N)
MAGASVKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSYWSHT
SPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMGKQEKDQQGIIP
QLCEDLFSRINDTTNDNMSYSVEVSYMEIYCERVRDLLNPKNKGNLRVREHPLLGPYVED
LSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAETNITTEK
VSKISLVDLAGSERADSTGAKGTRLKEGANINKSLTTLGKVISALAEMDSGPNKNKKKKK
TDFIPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAKQIRCNAVI
NEDLNNKLIRELKDEVTRLRDLLYAQGLGDITDGAGVKQLEDKVEELASKNYHLENEVAR
LKKLVEFTSAWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	3
MG	Magnesium ion	Mg	4
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	2
TA1	Taxol	C47 H51 N O14	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

Primary citation

Cryo-EM unveils kinesin KIF1A's processivity mechanism and the impact of its pathogenic variant P305L. Benoit, M.P.M.H., Rao, L., Asenjo, A.B. et al. Nat Commun (2024) 15:5530-5530. DOI 10.1038/s41467-024-48720-4 · 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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