8UTQ: KIF1A[1-393] AMP-PNP bound one-head-bound state

KIF1A[1-393] AMP-PNP bound one-head-bound state in complex with a microtubule - class T1L02*. Determined by electron microscopy at 3.1 Å resolution. Released 12 Jun 2024.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Homo sapiens, Sus scrofa
Chains: 5
Atoms: 16,825
Mol. weight: 253.92 kDa
Ligands: TA1, GDP, GTP, ANP
Released: 12 Jun 2024

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

Secondary structure: helices and β-sheets

8UTQ contains 116 α-helices and 86 β-strands across 5 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: 25 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	7
α-helix	10-28	19
α-helix	38-41	4
β-strand	53-55	3	8
β-strand	61-63	3	8
β-strand	65-68	4	7
β-strand	69	1	9
α-helix	72-79	8
β-strand	93	1	9
α-helix	103-104	2
α-helix	105-109	5
α-helix	115-128	14
β-strand	132-138	7	7
α-helix	144-160	17
β-strand	165-171	7	7
α-helix	172-174	3
α-helix	183-189	7
α-helix	191-196	6
β-strand	200-204	5	7
α-helix	206-212	7
α-helix	213-217	5
α-helix	224-239	16
α-helix	240-242	3
β-strand	248	1	7
α-helix	252-257	6
β-strand	269-272	4	7
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	7
α-helix	325-337	13
β-strand	343	1	7
β-strand	351-356	6	7
α-helix	358-361	4
β-strand	373-381	9	7
α-helix	384-399	16
α-helix	405-409	5
α-helix	416-435	20
α-helix	438-439	2

Chain B: 24 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	10
α-helix	10-27	18
β-strand	30	1	11
β-strand	36	1	11
α-helix	41-44	4
α-helix	47-49	3
β-strand	51-53	3	12
β-strand	59-61	3	12
β-strand	63-66	4	10
α-helix	70-77	8
α-helix	82-84	3
α-helix	87-89	3
β-strand	90-91	2	10
α-helix	101-102	2
α-helix	103-107	5
α-helix	108-126	19
β-strand	130-138	9	10
α-helix	142-158	17
β-strand	163-170	8	10
α-helix	171-172	2
α-helix	181-192	12
β-strand	199-203	5	10
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
α-helix	238-240	3
β-strand	246	1	13
α-helix	250-257	8
β-strand	265-266	2	10
β-strand	267-271	5	13
α-helix	286-294	9
α-helix	305-307	3
β-strand	310-319	10	13
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	13
β-strand	349-354	6	13
β-strand	363-371	9	13
α-helix	374-389	16
α-helix	395-399	5
α-helix	405-425	21

Chain E: 27 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	14
α-helix	10-28	19
α-helix	37-42	6
β-strand	53-55	3	15
β-strand	61-63	3	15
β-strand	65-68	4	14
β-strand	69	1	16
α-helix	72-79	8
β-strand	93	1	16
α-helix	103-104	2
α-helix	105-109	5
α-helix	115-128	14
β-strand	132-140	9	14
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-171	7	14
α-helix	172-174	3
α-helix	183-196	14
β-strand	200-204	5	14
α-helix	206-212	7
α-helix	213-217	5
α-helix	224-239	16
α-helix	240-242	3
β-strand	248	1	17
α-helix	252-259	8
β-strand	269-272	4	17
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	17
α-helix	325-337	13
β-strand	343	1	17
β-strand	352-356	5	17
α-helix	359-361	3
α-helix	369-370	2
β-strand	373-381	9	17
α-helix	384-399	16
α-helix	405-409	5
α-helix	415-435	21
α-helix	438-439	2

Chain I: 24 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	18
α-helix	10-28	19
β-strand	30	1	19
β-strand	36	1	19
α-helix	47-49	3
β-strand	51-53	3	20
α-helix	54	1
β-strand	59-61	3	20
β-strand	64-67	4	18
α-helix	70-77	8
α-helix	82-84	3
α-helix	87-89	3
β-strand	90-92	3	18
α-helix	101-102	2
α-helix	103-107	5
α-helix	109-126	18
β-strand	130-138	9	18
α-helix	142-158	17
β-strand	163-169	7	18
α-helix	181-195	15
β-strand	199-202	4	18
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
α-helix	238-240	3
β-strand	246	1	21
α-helix	250-257	8
β-strand	265-266	2	18
β-strand	267-271	5	21
α-helix	276-279	4
α-helix	286-294	9
α-helix	305-307	3
β-strand	310-319	10	21
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	21
β-strand	349-354	6	21
β-strand	363-371	9	21
α-helix	374-389	16
α-helix	395-399	5
α-helix	405-423	19

Chain K: 16 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	11-12	2	1
α-helix	17-21	5
β-strand	28-31	4	2
β-strand	34-37	4	2
α-helix	46-47	2
β-strand	48-51	4	2
β-strand	56-57	2	1
α-helix	70-73	4
α-helix	74-78	5
α-helix	79-85	7
β-strand	90-97	8	1
β-strand	98	1	3
α-helix	103-107	5
β-strand	109	1	4
β-strand	116	1	4
α-helix	118-132	15
β-strand	135	1	1
β-strand	138-149	12	1
β-strand	154-155	2	1
β-strand	166	1	1
α-helix	167	1
β-strand	168-171	4	5
β-strand	175-178	4	5
β-strand	183-186	4	1
α-helix	189-202	14
β-strand	205-206	2	6
β-strand	214-215	2	6
β-strand	218-229	12	1
β-strand	240-248	9	1
α-helix	250-251	2
β-strand	252	1	3
α-helix	255-258	4
α-helix	263-294	32
α-helix	310-314	5
α-helix	316-319	4
β-strand	324-331	8	1
α-helix	338-349	12
α-helix	364-372	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kinesin-like protein KIF1A	K	protein	438	Homo sapiens	Q12756 (AlphaFold model)
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)

Sequence of entity 1 (K), FASTA

>8UTQ_1 Kinesin-like protein KIF1A (chains K)
MAGASVKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSYWSHT
SPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMGKQEKDQQGIIP
QLCEDLFSRINDTTNDNMSYSVEVSYMEIYCERVRDLLNPKNKGNLRVREHPLLGPYVED
LSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAETNITTEK
VSKISLVDLAGSERADSTGAKGTRLKEGANINKSLTTLGKVISALAEMDSGPNKNKKKKK
TDFIPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAKQIRCNAVI
NEDPNNKLIRELKDEVTRLRDLLYAQGLGDITDGAGVKQLEDKVEELASKNYHLENEVAR
LKKLVEFTSAWSHPQFEK

Sequence of entity 2 (A, E), FASTA

>8UTQ_2 Tubulin alpha-1B chain (chains A, E)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 3 (B, I), FASTA

>8UTQ_3 Tubulin beta-2B chain (chains B, I)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Ligands and cofactors

ID	Name	Formula	Copies
TA1	Taxol	C47 H51 N O14	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1
MG	Magnesium ion	Mg	3

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 Q12756 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4EJQ 1.89 Å, Crystal structure of KIF1A C-CC1-FHA
4EGX 2.51 Å, Crystal structure of KIF1A CC1-FHA tandem
8UTS 2.7 Å, KIF1A[1-393] APO in complex with a microtubule
9YA5 2.95 Å, KIF1A R350G bound to microtubules in two-heads-bound state with AMP-PNP
8UTU 3.0 Å, KIF1A[1-393] P305L mutant AMP-PNP bound one and two heads bound states merged, in…
8UTV 3.0 Å, KIF1A[1-393] P305L mutant ADP bound in complex with a microtubule
8UTN 3.1 Å, KIF1A[1-393] AMP-PNP bound two-heads-bound state in complex with a microtubule (class…
8UTT 3.1 Å, KIF1A[1-393] P305L mutant AMP-PNP bound two-heads-bound state in complex with a…
9YAI 3.12 Å, KIF1A R350W bound to microtubules in two-heads-bound state with AMP-PNP
8UTO 3.2 Å, KIF1A[1-393] AMP-PNP bound two-heads-bound state in complex with a microtubule - class…
8UTP 3.2 Å, KIF1A[1-393] - AMP-PNP two-heads-bound state in complex with a microtubule - class T3L1
9YAB 3.21 Å, KIF1A R350W bound to microtubules in the apo state

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