8UTU: Kinesin-like protein KIF1A

KIF1A[1-393] P305L mutant AMP-PNP bound one and two heads bound states merged, in complex with a microtubule. Determined by electron microscopy at 3.0 Å resolution. Released 12 Jun 2024.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Homo sapiens, Sus scrofa
Chains: 4
Atoms: 13,615
Mol. weight: 202.64 kDa
Ligands: MG, ANP, GTP, GDP
Released: 12 Jun 2024

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

Secondary structure: helices and β-sheets

8UTU contains 87 α-helices and 75 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, 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	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-171	7	10
α-helix	172-174	3
α-helix	183-189	7
α-helix	191-196	6
β-strand	200-204	5	10
α-helix	206-215	10
α-helix	224-243	20
β-strand	248	1	13
α-helix	252-259	8
α-helix	263-265	3
β-strand	269-272	4	13
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	13
α-helix	325-337	13
β-strand	343	1	13
β-strand	351-356	6	13
α-helix	358-361	4
α-helix	369-370	2
β-strand	373-381	9	13
α-helix	384-399	16
α-helix	406-409	4
α-helix	416-431	16

Chain B: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	14
α-helix	10-28	19
β-strand	30	1	15
β-strand	36	1	15
α-helix	47-49	3
β-strand	51-54	4	16
β-strand	58-61	4	16
β-strand	65-66	2	14
α-helix	70-77	8
α-helix	87-89	3
β-strand	90-91	2	14
α-helix	101-102	2
α-helix	103-107	5
α-helix	109-125	17
β-strand	130-138	9	14
α-helix	142-158	17
β-strand	163-170	8	14
α-helix	181-192	12
β-strand	198-203	6	14
α-helix	204-213	10
α-helix	222-241	20
β-strand	244-246	3	17
α-helix	250-257	8
β-strand	265-266	2	14
β-strand	267-271	5	17
α-helix	286-293	8
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	374-389	16
α-helix	396-399	4
α-helix	405-424	20

Chain E: 23 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	18
α-helix	10-28	19
α-helix	37-42	6
β-strand	53-55	3	19
β-strand	61-63	3	19
β-strand	65-68	4	18
β-strand	69	1	20
α-helix	72-79	8
β-strand	93	1	20
α-helix	103-108	6
α-helix	115-128	14
β-strand	132-140	9	18
α-helix	144-160	17
β-strand	165-171	7	18
α-helix	172-174	3
α-helix	183-196	14
β-strand	200-204	5	18
α-helix	206-215	10
α-helix	224-243	20
β-strand	248	1	21
α-helix	252-259	8
β-strand	269-272	4	21
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	21
α-helix	325-337	13
β-strand	343	1	21
β-strand	352-356	5	21
α-helix	358-361	4
α-helix	368-370	3
β-strand	373-381	9	21
α-helix	384-399	16
α-helix	406-409	4
α-helix	415-417	3
α-helix	419-436	18
α-helix	438-440	3

Chain K: 18 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
α-helix	6	1
β-strand	7-12	6	2
α-helix	17-21	5
β-strand	26	1	3
β-strand	28-31	4	4
β-strand	34-37	4	4
β-strand	48-51	4	4
β-strand	54-57	4	2
β-strand	67	1	2
α-helix	70-73	4
α-helix	74-78	5
α-helix	79-87	9
β-strand	91-96	6	2
β-strand	98	1	5
α-helix	103-107	5
β-strand	109	1	6
β-strand	116	1	6
α-helix	120-133	14
β-strand	135	1	7
β-strand	138	1	7
β-strand	139-149	11	2
β-strand	154-156	3	2
α-helix	165	1
β-strand	166	1	2
α-helix	167	1
β-strand	168-171	4	8
β-strand	175-178	4	8
β-strand	184-186	3	2
α-helix	189-202	14
β-strand	205-206	2	9
β-strand	214-215	2	9
β-strand	218-228	11	2
β-strand	240-248	9	2
α-helix	249-251	3
β-strand	252	1	5
α-helix	253	1
α-helix	263-294	32
α-helix	310-314	5
α-helix	316-319	4
β-strand	324-331	8	2
β-strand	334	1	3
α-helix	335-337	3
α-helix	338-352	15
β-strand	355	1	1
α-helix	364-385	22

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	protein	445	Sus scrofa	A0A8D1UIR5 (AlphaFold model)

Sequence of entity 1 (K), FASTA

>8UTU_1 Kinesin-like protein KIF1A (chains K)
MAGASVKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSYWSHT
SPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMGKQEKDQQGIIP
QLCEDLFSRINDTTNDNMSYSVEVSYMEIYCERVRDLLNPKNKGNLRVREHPLLGPYVED
LSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAETNITTEK
VSKISLVDLAGSERADSTGAKGTRLKEGANINKSLTTLGKVISALAEMDSGPNKNKKKKK
TDFILYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAKQIRCNAVI
NEDPNNKLIRELKDEVTRLRDLLYAQGLGDITDGAGVKQLEDKVEELASKNYHLENEVAR
LKKLVEFTSAWSHPQFEK

Sequence of entity 2 (A, E), FASTA

>8UTU_2 Tubulin alpha-1B chain (chains A, E)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 3 (B), FASTA

>8UTU_3 Tubulin beta-2B chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Ligands and cofactors

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

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
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…
8UTQ 3.1 Å, KIF1A[1-393] AMP-PNP bound one-head-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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