9L7M: Nucleotide-free kinesin-1 motor domain

Nucleotide-free kinesin-1 motor domain bound to the microtubule. Determined by electron microscopy at 3.48 Å resolution. Released 23 Apr 2025.

Method: Electron microscopy
Resolution: 3.48 Å
Organisms: Sus scrofa, Homo sapiens
Chains: 5
Atoms: 16,181
Mol. weight: 242.68 kDa
Ligands: GTP, MG
Released: 23 Apr 2025

Explore 9L7M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9L7M contains 108 α-helices and 99 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.

Chains A and C: 23 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	10-27	18
α-helix	50-52	3
β-strand	55-56	2	2
β-strand	60-61	2	2
β-strand	65-68	4	1
α-helix	75-80	6
α-helix	104	1
α-helix	105-109	5
α-helix	115-123	9
β-strand	132-138	7	1
β-strand	139-140	2	3
α-helix	145-149	5
α-helix	150-159	10
β-strand	165-167	3	1
β-strand	169-171	3	3
α-helix	183-189	7
α-helix	193-196	4
β-strand	202-204	3	3
α-helix	207-211	5
α-helix	212-216	5
α-helix	224-233	10
α-helix	235-238	4
β-strand	248	1	4
α-helix	254-259	6
β-strand	269-270	2	5
β-strand	273	1	6
α-helix	288-291	4
α-helix	294-296	3
β-strand	312	1	7
β-strand	317-318	2	8
β-strand	320-321	2	9
α-helix	327-337	11
β-strand	343	1	7
β-strand	353-354	2	8
β-strand	355	1	4
α-helix	359-360	2
β-strand	373-374	2	9
β-strand	375	1	6
β-strand	377	1	8
β-strand	378-379	2	5
β-strand	381	1	7
α-helix	383-386	4
α-helix	388-392	5
α-helix	405-409	5
α-helix	416-434	19

Chains B and D: 26 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	10
α-helix	11-27	17
β-strand	30	1	11
β-strand	36	1	11
α-helix	43-47	3
α-helix	49-51	3
β-strand	53-56	4	12
β-strand	60-63	4	12
β-strand	65-69	5	10
α-helix	74-80	7
β-strand	93-94	2	10
α-helix	104-107	4
α-helix	116-122	7
β-strand	134-140	7	10
α-helix	145-150	6
α-helix	151-157	7
β-strand	165-166	2	10
β-strand	169-172	4	10
α-helix	175-177	3
α-helix	183-194	12
β-strand	201-205	5	10
α-helix	206-214	9
α-helix	224-226	3
α-helix	228-238	11
β-strand	248	1	13
α-helix	252-258	7
β-strand	267-268	2	10
β-strand	269-273	5	13
α-helix	281-283	3
α-helix	288-294	7
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-320	9	13
α-helix	325-337	13
β-strand	343	1	13
β-strand	351-355	5	13
α-helix	359	1
β-strand	374-381	8	13
α-helix	382-385	4
α-helix	387-396	10
α-helix	399-401	3
α-helix	406-409	4
α-helix	416-423	8
α-helix	427-433	7

Chain K: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	27
α-helix	21-25	5
α-helix	27-29	3
β-strand	33-34	2	28
β-strand	38-41	4	28
β-strand	44-47	4	28
β-strand	51-52	2	27
α-helix	58-65	8
α-helix	71-74	4
β-strand	79-85	7	27
α-helix	91-94	4
β-strand	97	1	29
β-strand	105	1	29
α-helix	109-120	12
β-strand	126-138	13	27
β-strand	141-144	4	27
β-strand	153	1	27
β-strand	155-156	2	30
β-strand	164-165	2	30
β-strand	171-173	3	27
α-helix	176-187	12
β-strand	205-216	12	27
β-strand	222-231	10	27
α-helix	246-270	25
α-helix	281-286	6
β-strand	295-302	8	27
α-helix	309-321	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A, C	protein	451	Sus scrofa	Q2XVP4 (AlphaFold model)
Tubulin beta chain	B, D	protein	445	Sus scrofa	P02554 (AlphaFold model)
Kinesin-1 heavy chain	K	protein	357	Homo sapiens	P33176 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9L7M_1 Tubulin alpha-1B chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D), FASTA

>9L7M_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA

Sequence of entity 3 (K), FASTA

>9L7M_3 Kinesin-1 heavy chain (chains K)
MADLAECNIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIASKPYAFDRVFQSSTSQEQ
VYNDCAKKIVKDVLEGYNGTIFAYGQTSSGKTHTMEGKLHDPEGMGIIPRIVQDIFNYIY
SMDENLEFHIKVSYFEIYLDKIRDLLDVSKTNLSVHEDKNRVPYVKGCTERFVCSPDEVM
DTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVSK
TGAEGAVLDEAKNINKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNCRTTIVI
CCSPSSYNESETKSTLLFGQRAKTIKNTVSVNVELTAEQWKKKYEKCKEGTHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	4
MG	Magnesium ion	Mg	4

Primary citation

Tension-induced suppression of allosteric conformational changes coordinates kinesin-1 stepping. Makino, T., Kanada, R., Mori, T. et al. J Cell Biol (2025) 224. DOI 10.1083/jcb.202501253 · 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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