5OGC: Kinesin-like protein KIF18A

Molecular basis of human kinesin-8 function and inhibition. Determined by electron microscopy at 4.8 Å resolution. Released 25 Oct 2017.

Method: Electron microscopy
Resolution: 4.8 Å
Organisms: Homo sapiens, Bos taurus, Sus scrofa
Chains: 3
Atoms: 9,290
Mol. weight: 144.44 kDa
Ligands: TA1, GDP, GTP, MG
Released: 25 Oct 2017

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

Secondary structure: helices and β-sheets

5OGC contains 59 α-helices and 45 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, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	5
α-helix	10-28	19
β-strand	65-69	5	5
α-helix	72-80	9
β-strand	92-94	3	5
α-helix	103-107	5
α-helix	111-128	18
β-strand	134-139	6	5
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-170	6	5
α-helix	183-195	13
β-strand	202-203	2	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	293-295	3
α-helix	298-300	3
β-strand	312-321	10	5
α-helix	325-336	12
β-strand	351-355	5	5
α-helix	359-360	2
β-strand	368	1	6
β-strand	373-381	9	5
α-helix	384-399	16
α-helix	403-405	3
α-helix	406-409	4
α-helix	415-434	20

Chain B: 24 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	53-55	3	9
β-strand	61-63	3	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	110-126	17
β-strand	132-140	9	7
α-helix	144-149	6
α-helix	150-160	11
β-strand	165-171	7	7
α-helix	172-174	3
α-helix	184-194	11
β-strand	200-203	4	7
α-helix	206-211	6
α-helix	212-216	5
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	327-338	12
α-helix	340-342	3
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: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	12-18	7	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	78-80	3	1
α-helix	86-89	4
α-helix	90-94	5
α-helix	95-103	9
β-strand	107-111	5	1
α-helix	119-123	5
α-helix	132-150	19
β-strand	153-163	11	1
β-strand	166-169	4	1
α-helix	177-178	2
β-strand	179-181	3	3
β-strand	187-189	3	3
β-strand	195	1	1
α-helix	200-213	14
α-helix	215-216	2
β-strand	217	1	4
β-strand	223	1	4
β-strand	229-238	10	1
α-helix	248-249	2
β-strand	250-258	9	1
α-helix	260-263	4
α-helix	265-268	4
α-helix	272-300	29
α-helix	307-309	3
α-helix	311-320	10
β-strand	326-332	7	1
α-helix	338-354	17

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

>5OGC_1 Kinesin-like protein KIF18A (chains K)
GSHMSVTEEDLCHHMKVVVRVRPENTKEKAAGFHKVVHVVDKHILVFDPKQEEVSFFHGK
KTTNQNVIKKQNKDLKFVFDAVFDETSTQSEVFEHTTKPILRSFLNGYNCTVLAYGATGA
GKTHTMLGSADEPGVMYLTMLHLYKCMDEIKEEKICSTAVSYLEVYNEQIRDLLVNSGPL
AVREDTQKGVVVHGLTLHQPKSSEEILHLLDNGNKNRTQHPTDMNATSSRSHAVFQIYLR
QQDKTASINQNVRIAKMSLIDLAGSERASTSGAKGTRFVEGTNINRSLLALGNVINALAD
SKRKNQHIPYRNSKLTRLLKDSLGGNCQTIMIAAVSPSSVFYDDTYNTLKYANRAKDIKS
SLKSNVLNVNNHITQYV

Sequence of entity 2 (A), FASTA

>5OGC_2 Tubulin alpha chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 3 (B), FASTA

>5OGC_3 Tubulin beta chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA

Ligands and cofactors

ID	Name	Formula	Copies
TA1	Taxol	C47 H51 N O14	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	1
9V5	4-chloranyl-2-nitro-1-(phenylsulfonyl)benzene	C12 H8 Cl N O4 S	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
7RSI 4.9 Å, The cryo-EM map of KIF18A bound to KIFBP
5OCU 5.2 Å, Molecular basis of human kinesin-8 function and inhibition
5OAM 5.5 Å, Molecular basis of human kinesin-8 function and inhibition

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