6ZPI: Microtubule

Microtubule complexed with Kif15 motor domain. Symmetrised asymmetric unit. Determined by electron microscopy at 4.5 Å resolution. Released 30 Dec 2020.

Method: Electron microscopy
Resolution: 4.5 Å
Organisms: Homo sapiens, Sus scrofa
Chains: 3
Atoms: 9,412
Mol. weight: 140.51 kDa
Ligands: TA1, GDP, GTP, MG
Released: 30 Dec 2020

Explore 6ZPI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZPI contains 58 α-helices and 55 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: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	7
α-helix	10-28	19
β-strand	53-55	3	8
β-strand	61-63	3	8
β-strand	65-69	5	7
α-helix	72-80	9
β-strand	92-94	3	7
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-126	16
β-strand	131-138	8	7
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165	1	7
β-strand	167-171	5	7
α-helix	172-174	3
α-helix	183-194	12
β-strand	200-204	5	7
α-helix	206-215	10
α-helix	224-243	20
α-helix	252-258	7
β-strand	269	1	7
β-strand	272-273	2	9
α-helix	288-295	8
β-strand	312-321	10	7
α-helix	325-337	13
β-strand	343	1	7
β-strand	351-356	6	7
α-helix	359-360	2
α-helix	362-363	2
β-strand	373-374	2	7
β-strand	375-376	2	9
β-strand	377-381	5	7
α-helix	385-401	17
α-helix	406-409	4
α-helix	415-436	22

Chain B: 23 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	10
α-helix	11-27	17
β-strand	30	1	11
β-strand	36	1	11
α-helix	42-47	4
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	73-80	8
α-helix	83-86	4
α-helix	89-91	3
β-strand	92-94	3	10
α-helix	103-107	5
α-helix	110-127	18
β-strand	132-140	9	10
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	10
α-helix	183-197	15
β-strand	200-205	6	10
α-helix	206-215	10
α-helix	224-243	20
α-helix	252-259	8
β-strand	267-268	2	10
β-strand	269-273	5	13
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	13
β-strand	312-320	9	13
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	13
β-strand	351-356	6	13
α-helix	359-360	2
β-strand	374-381	8	13
α-helix	382-384	3
α-helix	385-400	16
α-helix	406-409	4
α-helix	415-434	20

Chain C: 15 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	1
α-helix	27	1
β-strand	28-33	6	2
α-helix	34-37	4
β-strand	51-55	5	3
β-strand	58-61	4	3
β-strand	68-71	4	3
β-strand	74-76	3	2
α-helix	82-85	4
α-helix	86-90	5
α-helix	91-98	8
β-strand	103-109	7	2
β-strand	110	1	4
α-helix	115-119	5
α-helix	129-132	4
α-helix	135-151	17
β-strand	158-170	13	2
β-strand	173-176	4	2
β-strand	186-188	3	5
β-strand	196-198	3	5
β-strand	203-204	2	2
α-helix	208-221	14
β-strand	224	1	6
β-strand	234	1	6
β-strand	237-248	12	2
β-strand	255-265	11	2
β-strand	269	1	4
α-helix	272-275	4
α-helix	280-306	27
α-helix	315-317	3
α-helix	319-323	5
β-strand	333-340	8	2
α-helix	344-346	3
α-helix	347-362	16
β-strand	364-365	2	1
β-strand	371-372	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kinesin-like protein KIF15	C	protein	377	Homo sapiens	Q9NS87 (AlphaFold model)
Tubulin alpha-1B chain	A	protein	437	Sus scrofa	Q2XVP4 (AlphaFold model)
Tubulin beta chain	B	protein	431	Sus scrofa	P02554 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>6ZPI_1 Kinesin-like protein KIF15 (chains C)
MAPGSKTELRSVTNGQSNQPSNEGDAIKVFVRIRPPAERSGSADGEQNLSLSVLSSTSLR
LHSNPEPKTFTFDHVADVDTTQESVFATVAKSIVESCMSGYNGTIFAYGQTGSGKTFTMM
GPSESDNFSHNLRGVIPRSFEYLFSLIDREKEKAGAGKSFLSKCSFIEIYNEQIYDLLDS
ASAGLYLREHIKKGVFVVGAVEQVVTSAAEAYQVLSGGWRNRRVASTSMNRESSRSHAVF
TITIESMEKCNEIVNIRTSLLNLVDLAGSERQKDTHAEGMRLKEAGNINRSLSTLGQVIT
ALVDVGNGKQRHVSYRDSKLTFLLRDSLGGNAKTAIIANVHPGSRSFGETLSTLNFAQRA
KLIKNKAVVNEDTQCLE

Sequence of entity 2 (A), FASTA

>6ZPI_2 Tubulin alpha-1B chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGV

Sequence of entity 3 (B), FASTA

>6ZPI_3 Tubulin beta chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAD

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	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1

Primary citation

The mechanism of kinesin inhibition by kinesin-binding protein. Atherton, J., Hummel, J.J., Olieric, N. et al. Elife (2020) 9. DOI 10.7554/eLife.61481 · PubMed

Other PDB entries of the same protein (UniProt Q9NS87 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4BN2 2.69 Å, The crystal structure of kinesin-like protein KIF15
7RYP 4.8 Å, Cryo-EM structure of KIFBP:KIF15
6ZPH 6.9 Å, Kinesin binding protein complexed with Kif15 motor domain

Browse structure collections

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