5MIO: KIF2C-darpin fusion protein

KIF2C-darpin fusion protein bound to tubulin. Determined by X-ray diffraction at 3.19 Å resolution. Released 19 Jul 2017.

Method: X-ray diffraction
Resolution: 3.19 Å
Organisms: Bos taurus, Ovis aries, Homo sapiens
Chains: 3
Atoms: 10,421
Mol. weight: 164.24 kDa
Ligands: ANP, LOC, GDP, MG
Released: 19 Jul 2017

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

Secondary structure: helices and β-sheets

5MIO contains 77 α-helices and 58 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: 26 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-28	19
β-strand	35	1	2
α-helix	48-51	4
β-strand	53-55	3	3
β-strand	60	1	2
β-strand	61-63	3	3
β-strand	65-69	5	1
α-helix	73-79	7
α-helix	89-91	3
β-strand	92-94	3	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-126	16
β-strand	134-140	7	1
α-helix	144-160	17
β-strand	165-172	8	1
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	1
α-helix	206-215	10
α-helix	224-243	20
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	4
β-strand	277	1	5
α-helix	284-287	4
α-helix	288-293	6
α-helix	294-296	3
α-helix	298-300	3
β-strand	301	1	4
α-helix	307-309	3
β-strand	312-321	10	4
α-helix	325-336	12
β-strand	343	1	4
β-strand	352-356	5	4
α-helix	359-361	3
β-strand	368	1	5
α-helix	369-370	2
β-strand	373-381	9	4
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	415-435	21

Chain B: 26 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	6
α-helix	10-27	18
β-strand	30	1	7
β-strand	35	1	8
β-strand	36	1	7
α-helix	41-45	3
α-helix	49-51	3
β-strand	53-55	3	9
β-strand	60	1	8
β-strand	61-63	3	9
β-strand	65-69	5	6
α-helix	73-79	7
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	6
α-helix	103-107	5
α-helix	110-127	18
β-strand	132-140	9	6
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	6
α-helix	173	1
β-strand	174	1	10
β-strand	177	1	10
α-helix	183-197	15
β-strand	200-205	6	6
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-238	15
α-helix	240-243	4
α-helix	252-259	8
β-strand	267-268	2	6
β-strand	269-273	5	11
α-helix	285-287	3
α-helix	288-296	9
α-helix	298-300	3
β-strand	301	1	11
β-strand	312-321	10	11
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	11
β-strand	351-356	6	11
β-strand	373-381	9	11
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-436	22

Chain C: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	230-242	13
β-strand	260-265	6	12
α-helix	266-269	4
α-helix	270-274	5
α-helix	277-278	2
β-strand	279	1	13
β-strand	281-282	2	14
β-strand	288-296	9	14
β-strand	302-310	9	14
β-strand	313-315	3	12
α-helix	321-327	7
α-helix	330-337	8
β-strand	341-347	7	12
α-helix	354-359	6
α-helix	373-385	13
α-helix	388-391	4
β-strand	395-405	11	12
β-strand	408-411	4	12
β-strand	417-418	2	12
β-strand	420-423	4	15
β-strand	429-432	4	15
α-helix	434-436	3
β-strand	437-439	3	12
α-helix	442-455	14
β-strand	458-459	2	16
β-strand	467-468	2	16
β-strand	471-480	10	12
β-strand	483-492	10	12
α-helix	493-495	3
α-helix	508-532	25
α-helix	543-547	5
α-helix	549-552	4
β-strand	558-565	8	12
β-strand	568	1	13
α-helix	569-571	3
α-helix	572-583	12
α-helix	623-633	11
α-helix	636-643	8
α-helix	659-665	7
α-helix	669-677	9
α-helix	692-699	8
α-helix	702-710	9
α-helix	725-731	7
α-helix	735-743	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A	protein	451	Bos taurus	P81947 (AlphaFold model)
Tubulin beta chain	B	protein	445	Ovis aries	D0VWY9 (AlphaFold model)
Kinesin-like protein KIF2C,KIF2C FUSED TO A DARPIN,KIF2C FUSED TO A DARPIN	C	protein	573	Homo sapiens	Q99661 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5MIO_1 Tubulin alpha-1B chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B), FASTA

>5MIO_2 Tubulin beta chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (C), FASTA

>5MIO_3 Kinesin-like protein KIF2C,KIF2C FUSED TO A DARPIN,KIF2C FUSED TO A DARPIN (chains C)
MGRMKRAQEYDSSFPNWEFARMIKEFRATLECHPLTMTDPIEEHRICVCVRKRPLNKQEL
AKKEIDVISIPSKCLLLVHEPKLKVDLTKYLENQAFCFDFAFDETASNEVVYRFTAAPLV
QTIFEGGKATCFAYGQTGSGKTHTMGGDLSGKAQNASKGIYAMASADVFLLKNQPCYRKL
GLEVYVTFFEIYNGKLFDLLNKKAKLRVLEDGKQQVQVVGLQEHLVNSADDVIKMIDMGS
ACRTSGQTFANSNSSRSHACFQIILRAKGRMHGKFSLVDLAGNERGADTSSADRQTRMEG
AEINKSLLALKECIRALGQNKAHTPFRESKLTQVLRDSFIGENSRTCMIATISPGISSCE
YTLNTLRYADRVKELSPHSGPSGEQGGGGSGGGGSGGGGSGGGGSGGSDLGKKLLEAARA
GQDDEVRVLMANGADVNATDASGLTPLHLAATYGHLEIVEVLLKHGADVSASDLMGSTPL
HLAALIGHLEIVEVLLKHGADVNAVDTWGDTPLRLAAVMGHLKIVEALLKHGADVNAQDK
FGKTAYDTSIDNGSEDLAEILQKLNLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1
LOC	N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethana…	C22 H25 N O6	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
MG	Magnesium ion	Mg	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1

Primary citation

Insight into microtubule disassembly by kinesin-13s from the structure of Kif2C bound to tubulin. Wang, W., Cantos-Fernandes, S., Lv, Y. et al. Nat Commun (2017) 8:70-70. DOI 10.1038/s41467-017-00091-9 · PubMed

Other PDB entries of the same protein (UniProt P81947 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6S8K 1.52 Å, Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes
8QL2 1.7 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
6ZWB 1.75 Å, Z-SBTub3 photoswitch bound to tubulin-DARPin D1 complex
4I4T 1.8 Å, Crystal structure of tubulin-RB3-TTL-Zampanolide complex
5IYZ 1.8 Å, Tubulin-MMAE complex
5NQU 1.8 Å, Tubulin Darpin cryo structure
7YZ3 1.8 Å, Molecular snapshots of drug release from tubulin: Apo state
8QEA 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
8QL3 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
8QL4 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
8QL5 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
8QL6 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…

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