8UTV: KIF1A[1-393] P305L mutant ADP bound

KIF1A[1-393] P305L mutant ADP bound 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: Sus scrofa, Homo sapiens
Chains: 4
Atoms: 13,337
Mol. weight: 202.53 kDa
Ligands: ADP, TA1, GDP, MG
Released: 12 Jun 2024

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

Secondary structure: helices and β-sheets

8UTV contains 88 α-helices and 67 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	4
α-helix	10-28	19
α-helix	38-42	5
β-strand	53-55	3	5
β-strand	61-63	3	5
β-strand	65-68	4	4
β-strand	69	1	6
α-helix	72-80	9
α-helix	82-85	4
β-strand	93	1	6
α-helix	103-104	2
α-helix	105-109	5
α-helix	114-128	15
β-strand	132-140	9	4
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	4
α-helix	173-174	2
α-helix	183-189	7
α-helix	191-196	6
β-strand	200-205	6	4
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	288-295	8
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-321	10	4
α-helix	325-337	13
β-strand	343	1	4
β-strand	351-356	6	4
α-helix	359-360	2
α-helix	368-370	3
β-strand	373-381	9	4
α-helix	384-399	16
α-helix	405-409	5
α-helix	417-435	19
α-helix	438-439	2

Chain B: 24 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	7
α-helix	10-27	18
β-strand	30	1	8
β-strand	36	1	8
α-helix	47-49	3
β-strand	51-54	4	9
β-strand	58-61	4	9
β-strand	63-66	4	7
α-helix	70-77	8
α-helix	82-84	3
α-helix	87-89	3
β-strand	90-91	2	7
α-helix	103-107	5
α-helix	109-125	17
β-strand	130-138	9	7
α-helix	143-158	16
β-strand	163-169	7	7
α-helix	181-192	12
β-strand	200-202	3	7
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
α-helix	238-240	3
β-strand	246	1	10
α-helix	250-257	8
β-strand	266	1	7
β-strand	267-271	5	10
α-helix	279-281	3
α-helix	286-293	8
α-helix	296-298	3
α-helix	305-307	3
β-strand	310-318	9	10
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	10
β-strand	349-354	6	10
β-strand	364-371	8	10
α-helix	372-374	3
α-helix	375-389	15
α-helix	395-399	5
α-helix	405-424	20

Chain E: 25 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	10-28	19
α-helix	38-42	5
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	72-80	9
α-helix	82-85	4
β-strand	93	1	3
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-128	18
β-strand	132-140	9	1
α-helix	145-160	16
β-strand	165-171	7	1
α-helix	172-174	3
α-helix	183-189	7
α-helix	191-196	6
β-strand	200-204	5	1
α-helix	206-212	7
α-helix	213-217	5
α-helix	224-243	20
β-strand	248	1	1
α-helix	252-259	8
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	325-337	13
β-strand	343	1	1
β-strand	351-356	6	1
α-helix	359-360	2
α-helix	368-370	3
β-strand	373-381	9	1
α-helix	384-399	16
α-helix	405-409	5
α-helix	417-435	19

Chain K: 13 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	11
α-helix	13-15	3
α-helix	17-21	5
β-strand	28-31	4	12
β-strand	34-37	4	12
β-strand	48-51	4	12
β-strand	54-56	3	11
α-helix	70-73	4
α-helix	74-78	5
α-helix	79-86	8
β-strand	91-96	6	11
α-helix	103-107	5
β-strand	109	1	13
β-strand	116	1	13
α-helix	118-132	15
β-strand	138-150	13	11
β-strand	153-156	4	11
β-strand	166	1	11
β-strand	168-171	4	14
β-strand	175-178	4	14
β-strand	184-185	2	11
α-helix	189-200	12
β-strand	205-206	2	15
β-strand	214-215	2	15
β-strand	218-229	12	11
β-strand	241-248	8	11
α-helix	249-252	4
α-helix	263-295	33
α-helix	310-314	5
α-helix	316-319	4
β-strand	324-331	8	11
α-helix	338-349	12
β-strand	354	1	12

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	protein	445	Sus scrofa	A0A8D1UIR5 (AlphaFold model)
Kinesin-like protein KIF1A	K	protein	438	Homo sapiens	Q12756 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>8UTV_1 Tubulin alpha-1B chain (chains A, E)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B), FASTA

>8UTV_2 Tubulin beta-2B chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (K), FASTA

>8UTV_3 Kinesin-like protein KIF1A (chains K)
MAGASVKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSYWSHT
SPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMGKQEKDQQGIIP
QLCEDLFSRINDTTNDNMSYSVEVSYMEIYCERVRDLLNPKNKGNLRVREHPLLGPYVED
LSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAETNITTEK
VSKISLVDLAGSERADSTGAKGTRLKEGANINKSLTTLGKVISALAEMDSGPNKNKKKKK
TDFILYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAKQIRCNAVI
NEDPNNKLIRELKDEVTRLRDLLYAQGLGDITDGAGVKQLEDKVEELASKNYHLENEVAR
LKKLVEFTSAWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
TA1	Taxol	C47 H51 N O14	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
MG	Magnesium ion	Mg	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	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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