5OCU: Kinesin-like protein KIF18A

Molecular basis of human kinesin-8 function and inhibition. Determined by electron microscopy at 5.2 Å resolution. Released 25 Oct 2017.

Method: Electron microscopy
Resolution: 5.2 Å
Organisms: Homo sapiens, Bos taurus, Sus scrofa
Chains: 3
Atoms: 4,840
Mol. weight: 144.67 kDa
Ligands: MG, ANP, ZN, GTP
Released: 25 Oct 2017

Explore 5OCU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5OCU contains 59 α-helices and 47 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: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	5
α-helix	10-26	17
β-strand	65-69	5	5
α-helix	72-80	9
β-strand	92-94	3	5
α-helix	103-107	5
α-helix	109-128	20
β-strand	134-139	6	5
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-170	6	5
α-helix	184-195	12
β-strand	200-203	4	5
α-helix	206-215	10
α-helix	224-238	15
β-strand	248	1	5
α-helix	252-259	8
β-strand	269-270	2	5
β-strand	277	1	6
α-helix	288-291	4
α-helix	293-296	4
β-strand	312-321	10	5
α-helix	325-336	12
β-strand	343	1	5
β-strand	351-355	5	5
β-strand	368	1	6
β-strand	373-381	9	5
α-helix	382-384	3
α-helix	385-399	15
α-helix	403-405	3
α-helix	406-409	4
α-helix	415-429	15
α-helix	431-434	4

Chain B: 22 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	7
α-helix	10-26	17
β-strand	30	1	8
β-strand	36	1	8
α-helix	49-52	4
β-strand	55	1	9
β-strand	61	1	9
β-strand	65-69	5	7
α-helix	72-78	7
α-helix	83-85	3
α-helix	89-91	3
β-strand	92-94	3	7
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-114	4
α-helix	116-126	11
β-strand	132-140	9	7
α-helix	144-149	6
α-helix	150-160	11
β-strand	165-171	7	7
α-helix	184-194	11
β-strand	200-203	4	7
α-helix	206-214	9
α-helix	224-242	19
β-strand	248	1	10
α-helix	252-259	8
β-strand	267-268	2	7
β-strand	269-271	3	10
α-helix	289-295	7
α-helix	307-309	3
β-strand	312-320	9	10
α-helix	325-338	14
β-strand	351-356	6	10
β-strand	374-381	8	10
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-436	22

Chain K: 18 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	1
α-helix	23-28	6
β-strand	34-36	3	2
β-strand	41-44	4	2
β-strand	72-75	4	2
β-strand	78-79	2	1
α-helix	86-103	18
α-helix	105-106	2
β-strand	107-112	6	1
α-helix	119-123	5
α-helix	130-131	2
α-helix	132-146	15
β-strand	151-163	13	1
β-strand	166-169	4	1
α-helix	176-178	3
β-strand	179-181	3	3
β-strand	187-189	3	3
β-strand	195	1	1
α-helix	200-213	14
β-strand	216-217	2	4
β-strand	225-226	2	4
β-strand	229-240	12	1
α-helix	248	1
β-strand	249-258	10	1
α-helix	259-262	4
α-helix	265-268	4
α-helix	273-296	24
α-helix	298-301	4
α-helix	307-309	3
α-helix	311-316	6
α-helix	317-321	5
β-strand	326-332	7	1
α-helix	338-354	17
α-helix	356-359	4
β-strand	364	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kinesin-like protein KIF18A	K	protein	377	Homo sapiens	Q8NI77 (AlphaFold model)
Tubulin alpha chain	A	protein	451	Bos taurus	P81947 (AlphaFold model)
Tubulin beta chain	B	protein	445	Sus scrofa	P02554 (AlphaFold model)

Sequence of entity 1 (K), FASTA

>5OCU_1 Kinesin-like protein KIF18A (chains K)
GSHMSVTEEDLCHHMKVVVRVRPENTKEKAAGFHKVVHVVDKHILVFDPKQEEVSFFHGK
KTTNQNVIKKQNKDLKFVFDAVFDETSTQSEVFEHTTKPILRSFLNGYNCTVLAYGATGA
GKTHTMLGSADEPGVMYLTMLHLYKCMDEIKEEKICSTAVSYLEVYNEQIRDLLVNSGPL
AVREDTQKGVVVHGLTLHQPKSSEEILHLLDNGNKNRTQHPTDMNATSSRSHAVFQIYLR
QQDKTASINQNVRIAKMSLIDLAGSERASTSGAKGTRFVEGTNINRSLLALGNVINALAD
SKRKNQHIPYRNSKLTRLLKDSLGGNCQTIMIAAVSPSSVFYDDTYNTLKYANRAKDIKS
SLKSNVLNVNNHITQYV

Sequence of entity 2 (A), FASTA

>5OCU_2 Tubulin alpha chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 3 (B), FASTA

>5OCU_3 Tubulin beta chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1
ZN	Zinc ion	Zn	1
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

Primary citation

Structural basis of human kinesin-8 function and inhibition. Locke, J., Joseph, A.P., Pena, A. et al. Proc Natl Acad Sci U S A (2017) 114:E9539-E9548. DOI 10.1073/pnas.1712169114 · PubMed

Other PDB entries of the same protein (UniProt Q8NI77 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3LRE 2.2 Å, Crystal Structure Analysis of Human Kinesin-8 Motor Domain
9YMG 2.41 Å, Human KIF18A-DARPin fusion protein bound to AMP-PNP and tubulin
9DI0 3.1 Å, Cryo-EM structure of Kif18A bound to a microtubule
5OGC 4.8 Å, Molecular basis of human kinesin-8 function and inhibition
7RSI 4.9 Å, The cryo-EM map of KIF18A bound to KIFBP
5OAM 5.5 Å, Molecular basis of human kinesin-8 function and inhibition

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