9L78: Nucleotide-free human kinesin-1 motor domain

Crystal structure of nucleotide-free human kinesin-1 motor domain (G234A mutant). Determined by X-ray diffraction at 2.82 Å resolution. Released 23 Apr 2025.

Method: X-ray diffraction
Resolution: 2.82 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,762
Mol. weight: 76.61 kDa
Released: 23 Apr 2025

Explore 9L78 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9L78 contains 25 α-helices and 35 β-strands across 2 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: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	1
α-helix	17-19	3
α-helix	20-25	6
β-strand	31-34	4	2
β-strand	38-41	4	2
β-strand	44-47	4	2
β-strand	50-52	3	1
α-helix	58-65	8
α-helix	67-73	7
β-strand	79-85	7	1
α-helix	91-95	5
β-strand	97	1	3
β-strand	105	1	3
α-helix	107-119	13
β-strand	126-138	13	1
β-strand	141-144	4	1
β-strand	154-157	4	4
β-strand	163-166	4	4
β-strand	171-172	2	1
α-helix	176-188	13
β-strand	205-216	12	1
β-strand	221-231	11	1
α-helix	232-234	3
α-helix	247-270	24
α-helix	277-279	3
α-helix	282-285	4
α-helix	287-290	4
β-strand	295-302	8	1
α-helix	306-308	3
α-helix	309-322	14

Chain B: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	5
β-strand	29	1	6
β-strand	32-34	3	7
β-strand	38-41	4	7
β-strand	44-47	4	7
β-strand	50-52	3	5
α-helix	58-65	8
α-helix	67-73	7
β-strand	79-84	6	5
α-helix	91-95	5
β-strand	97	1	8
β-strand	105	1	8
α-helix	107-120	14
β-strand	126-138	13	5
β-strand	141-144	4	5
β-strand	151	1	5
β-strand	154-157	4	9
β-strand	163-166	4	9
β-strand	171-173	3	5
α-helix	176-188	13
β-strand	205-216	12	5
β-strand	222-231	10	5
α-helix	232-234	3
α-helix	247-269	23
α-helix	277-279	3
α-helix	282-285	4
α-helix	287-290	4
β-strand	295-302	8	5
β-strand	305	1	6
α-helix	309-320	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kinesin-1 heavy chain	A, B	protein	342	Homo sapiens	P33176 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9L78_1 Kinesin-1 heavy chain (chains A, B)
MHHHHHHADLAESNIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIASKPYAFDRVFQS
STSQEQVYNDAAKKIVKDVLEGYNGTIFAYGQTSSGKTHTMEGKLHDPEGMGIIPRIVQD
IFNYIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKTNLSVHEDKNRVPYVKGATERFVS
SPDEVMDTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAA
SEKVSKTGAEGAVLDEAKNINKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNA
RTTIVICCSPSSYNESETKSTLLFGQRAKTIKNTVSVNVELT

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 P33176 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1BG2 1.8 Å, Human ubiquitous kinesin motor domain
5LT1 1.95 Å, nucleotide-free kinesin-1 motor domain T92V mutant, P21 crystal form
5LT0 2.0 Å, nucleotide-free kinesin-1 motor domain, P212121 crystal form
4LNU 2.19 Å, Nucleotide-free kinesin motor domain in complex with tubulin and a DARPin
9L7E 2.4 Å, Crystal structure of human kinesin-1 motor domain (G234A mutant) in complex with ADP
5LT3 2.59 Å, nucleotide-free kinesin-1 motor domain T87A mutant, P1 crystal form
5LT2 2.6 Å, nucleotide-free kinesin-1 motor domain, P1 crystal form
1MKJ 2.7 Å, Human Kinesin Motor Domain With Docked Neck Linker
9L6K 2.8 Å, Crystal structure of nucleotide-free human kinesin-1 motor domain (G234V mutant)
5LT4 2.88 Å, nucleotide-free kinesin-1 motor domain T92V mutant, P1 crystal form
9GNQ 2.9 Å, Microtubule-associated Kif5B IAK tail mutant bound to ADP
7TR2 3.0 Å, Apo CaKip3[2-436]-L2-mutant(HsKHC) in complex with a microtubule

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