6TH4: Tubulin-inhibitor complex

Tubulin-inhibitor complex. Determined by X-ray diffraction at 2.12 Å resolution. Released 1 Dec 2021.

Method: X-ray diffraction
Resolution: 2.12 Å
Organisms: Ovis aries, Rattus norvegicus
Chains: 5
Atoms: 14,923
Mol. weight: 220.49 kDa
Ligands: GTP, MG, GDP, N9B
Released: 1 Dec 2021

Explore 6TH4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6TH4 contains 114 α-helices and 74 β-strands across 5 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: 28 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-28	19
α-helix	48-51	4
β-strand	53-55	3	2
β-strand	61-63	3	2
β-strand	65-69	5	1
α-helix	73-80	8
α-helix	89-91	3
β-strand	92-94	3	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-127	17
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	206-217	12
α-helix	224-243	20
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	3
β-strand	277	1	4
α-helix	284-287	4
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	3
α-helix	307-309	3
β-strand	312-321	10	3
α-helix	325-336	12
α-helix	342	1
β-strand	343	1	3
α-helix	344	1
β-strand	349-356	8	3
α-helix	359-361	3
β-strand	368	1	4
α-helix	369-370	2
β-strand	373-381	9	3
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	415-436	22
α-helix	438-439	2

Chain B: 28 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	5
α-helix	10-28	19
β-strand	30	1	6
β-strand	35	1	7
β-strand	36	1	6
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-56	4	7
β-strand	60-63	4	7
β-strand	65-69	5	5
α-helix	72-80	9
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	5
α-helix	103-104	2
α-helix	105-109	5
α-helix	110-127	18
β-strand	132-140	9	5
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	5
α-helix	173	1
β-strand	174	1	8
β-strand	177	1	8
α-helix	183-197	15
β-strand	200-205	6	5
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	5
β-strand	269-273	5	9
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	9
α-helix	307-309	3
β-strand	312-320	9	9
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	9
β-strand	351-356	6	9
α-helix	359-360	2
β-strand	374-381	8	9
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-437	23

Chain C: 29 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	10
α-helix	10-28	19
α-helix	48-51	4
β-strand	53-55	3	11
β-strand	61-63	3	11
β-strand	65-69	5	10
α-helix	73-80	8
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	115-126	12
β-strand	134-140	7	10
α-helix	144	1
α-helix	145-149	5
α-helix	150-161	12
β-strand	165-172	8	10
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	10
α-helix	206-215	10
α-helix	224-243	20
β-strand	248	1	12
α-helix	252-259	8
β-strand	262	1	13
β-strand	265	1	13
α-helix	268	1
β-strand	269-273	5	12
β-strand	277	1	14
α-helix	284-287	4
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	12
α-helix	307-309	3
β-strand	312-321	10	12
α-helix	325-336	12
β-strand	343	1	12
β-strand	351-356	6	12
α-helix	359-363	5
β-strand	368	1	14
α-helix	369-370	2
β-strand	373-381	9	12
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	415-436	22
α-helix	438-440	3

Chain D: 28 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	15
α-helix	10-28	19
β-strand	30	1	16
β-strand	36	1	16
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-56	4	17
β-strand	60-63	4	17
β-strand	65-69	5	15
α-helix	72-80	9
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	15
α-helix	103-104	2
α-helix	105-109	5
α-helix	110-127	18
β-strand	132-140	9	15
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	15
α-helix	173	1
α-helix	183-197	15
β-strand	200-205	6	15
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	15
β-strand	269-273	5	18
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	18
α-helix	307-309	3
β-strand	312-320	9	18
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	18
β-strand	351-356	6	18
α-helix	359-360	2
β-strand	374-381	8	18
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-437	23

Chain E: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	3
β-strand	17-25	9	3
α-helix	47-139	93

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha chain	A, C	protein	451	Ovis aries	A0A836D7T3 (AlphaFold model)
Tubulin beta chain	B, D	protein	445	Ovis aries	D0VWY9 (AlphaFold model)
Stathmin-4	E	protein	143	Rattus norvegicus	P63043 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6TH4_1 Tubulin alpha chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D), FASTA

>6TH4_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (E), FASTA

>6TH4_3 Stathmin-4 (chains E)
XADMEVIELNKATSGQSWEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRK
YQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLER
LQEKDKHAEEVRKNKELKEEASR

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
MG	Magnesium ion	Mg	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
N9B	1,2,3,9-tetramethoxy-6-methylidene-5~{H}-cyclohepta[a]naphthalen-8-one	C20 H20 O5	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

B-nor-methylene Colchicinoid PT-100 Selectively Induces Apoptosis in Multidrug-Resistant Human Cancer Cells via an Intrinsic Pathway in a Caspase-Independent Manner. Stein, A., Hilken nee Thomopoulou, P., Frias, C. et al. ACS Omega (2022) 7:2591-2603. DOI 10.1021/acsomega.1c04659

Other PDB entries of the same protein (UniProt A0A836D7T3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LNU 2.19 Å, Nucleotide-free kinesin motor domain in complex with tubulin and a DARPin
7Q1F 2.35 Å, CPAP:TUBULIN:IE5 alpharep complex
7Z0F 2.4 Å, Cpap:s-TUBULIN:IIH5 alpharep complex
8CGZ 2.53 Å, tubulin-AB8939 complex
7Q1E 2.7 Å, CPAP:TUBULIN:IIH5 alpharep complex
7Z0G 3.49 Å, CPAP:TUBULIN:IE5 alpharep complex P1 space group

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