9DI0: Kif18A

Cryo-EM structure of Kif18A bound to a microtubule. Determined by electron microscopy at 3.1 Å resolution. Released 16 Jul 2025.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Homo sapiens, Sus scrofa
Chains: 3
Atoms: 9,361
Mol. weight: 164.42 kDa
Ligands: GTP, GDP, TA1, MG
Released: 16 Jul 2025

Explore 9DI0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DI0 contains 59 α-helices and 53 β-strands across 3 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: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	1
α-helix	19-22	4
α-helix	23-26	4
β-strand	32	1	2
β-strand	34-38	5	3
β-strand	41-44	4	3
β-strand	72-74	3	3
β-strand	79-80	2	1
α-helix	87-92	6
β-strand	108-109	2	4
β-strand	110-111	2	1
α-helix	119-121	3
α-helix	122-126	5
β-strand	154-163	10	4
β-strand	166-169	4	4
β-strand	177	1	4
β-strand	178-180	3	5
β-strand	188-190	3	5
β-strand	195	1	4
α-helix	201-209	9
β-strand	229-237	9	4
β-strand	253-258	6	4
α-helix	280-294	15
α-helix	307-309	3
α-helix	311-315	5
α-helix	317-320	4
β-strand	327-332	6	1
β-strand	335	1	2
α-helix	348-352	5

Chain K: 25 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	6
α-helix	10-27	18
β-strand	30	1	7
β-strand	36	1	7
α-helix	41-45	5
α-helix	47-49	3
β-strand	51-54	4	8
β-strand	58-61	4	8
β-strand	63-67	5	6
α-helix	71-78	8
α-helix	87-89	3
β-strand	90-92	3	6
α-helix	101-102	2
α-helix	103-107	5
α-helix	109-125	17
β-strand	129-138	10	6
α-helix	143-158	16
β-strand	163-169	7	6
α-helix	170-172	3
α-helix	181-195	15
β-strand	198-202	5	6
α-helix	204-213	10
α-helix	222-236	15
α-helix	238-240	3
β-strand	246	1	9
α-helix	250-257	8
β-strand	265-266	2	6
β-strand	267-271	5	9
α-helix	286-293	8
α-helix	296-298	3
α-helix	305-307	3
β-strand	310-319	10	9
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	9
β-strand	349-354	6	9
α-helix	357-358	2
β-strand	363-371	9	9
α-helix	372-374	3
α-helix	375-390	16
α-helix	396-399	4
α-helix	405-424	20

Chain L: 23 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	10
α-helix	10-28	19
β-strand	35	1	11
β-strand	53-56	4	11
β-strand	60-63	4	11
β-strand	65-69	5	10
α-helix	72-80	9
α-helix	89-91	3
β-strand	92-94	3	10
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-128	14
β-strand	134-140	7	10
α-helix	144-160	17
β-strand	165-172	8	10
α-helix	173-174	2
α-helix	183-194	12
β-strand	202-205	4	10
α-helix	206-215	10
α-helix	224-243	20
β-strand	246	1	12
α-helix	252-259	8
β-strand	262	1	13
β-strand	265	1	13
β-strand	269-273	5	10
α-helix	278-281	4
α-helix	288-294	7
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-321	10	10
α-helix	325-337	13
β-strand	343	1	10
β-strand	351-355	5	10
β-strand	356	1	12
α-helix	359-361	3
β-strand	373-381	9	10
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-409	5
α-helix	416-435	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kinesin-like protein KIF18A, Methylated-DNA--protein-cysteine methyltransferase chimera	A	protein	562	Homo sapiens	P16455 (AlphaFold model), Q8NI77 (AlphaFold model)
Tubulin beta chain	K	protein	445	Sus scrofa	P02554 (AlphaFold model)
Tubulin alpha-1B chain	L	protein	451	Sus scrofa	Q2XVP4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9DI0_1 Kinesin-like protein KIF18A, Methylated-DNA--protein-cysteine methyltransferase chimera (chains A)
VGSEFELSVTEEDLCHHMKVVVRVRPENTKEKAAGFHKVVHVVDKHILVFDPKQEEVSFF
HGKKTTNQNVIKKQNKDLKFVFDAVFDETSTQSEVFEHTTKPILRSFLNGYNCTVLAYGA
TGAGKTHTMLGSADEPGVMYLTMLHLYKCMDEIKEEKICSTAVSYLEVYNEQIRDLLVNS
GPLAVREDTQKGVVVHGLTLHQPKSSEEILHLLDNGNKNRTQHPTDMNATSSRSHAVFQI
YLRQQDKTASINQNVRIAKMSLIDLAGSERASTSGAKGTRFVEGTNINRSLLALGNVINA
LADSKRKNQHIPYRNSKLTRLLKDSLGGNCQTIMIAAVSPSSVFYDDTYNTLKYANRAKD
IKSSLKSNVLNVNNHITQYVMDKDCEMKRTTLDSPLGKLELSGCEQGLHRIIFLGKGTSA
ADAVEVPAPAAVLGGPEPLMQATAWLNAYFHQPEAIEEFPVPALHHPVFQQESFTRQVLW
KLLKVVKFGEVISYSHLAALAGNPAATAAVKTALSGNPVPILIPCHRVVQGDLDVGGYEG
GLAVKEWLLAHEGHRLGKPGLG

Sequence of entity 2 (K), FASTA

>9DI0_2 Tubulin beta chain (chains K)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA

Sequence of entity 3 (L), FASTA

>9DI0_3 Tubulin alpha-1B chain (chains L)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Ligands and cofactors

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

Primary citation

HURP regulates Kif18A recruitment and activity to synergistically control microtubule dynamics. Perez-Bertoldi, J.M., Zhao, Y., Thawani, A. et al. Nat Commun (2024) 15:9687-9687. DOI 10.1038/s41467-024-53691-7 · PubMed

Other PDB entries of the same protein (UniProt P16455 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1QNT 1.9 Å, X-ray structure of human O6alkylguanine-DNA alkyltransferase
1EH6 2.0 Å, Human O6-alkylguanine-DNA alkyltransferase
1EH7 2.0 Å, Methylated human O6-alkylguanine-DNA alkyltransferase
9QF2 2.42 Å, Cryo-EM structure of the fully Coronin-1B-decorated actin filament in the ADP state.
1EH8 2.5 Å, Benzylated human O6-alkylguanine-DNA alkyltransferase
28OP 2.7 Å, Structure of the human inner kinetochore CCAN and CENP-C bound to DNA
9QEY 2.74 Å, Cryo-EM structure of the actin filament bound by a single Coronin-1B molecule.
9QFB 2.74 Å, Cryo-EM structure of the fully Coronin-1B-decorated actin filament in the ADP state.
9QFQ 2.76 Å, Cryo-EM structure of the cofilactin barbed end bound by AIP1
1YFH 3.01 Å, wt Human O6-Alkylguanine-DNA Alkyltransferase Bound To DNA Containing an Alkylated…
9QFE 3.12 Å, Cryo-EM structure of the actin filament hetero-decorated by Coronin-1 and Cofilin-1 on…
9QFW 3.16 Å, Cryo-EM structure of the cofilactin barbed end bound by two AIP1 molecules

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