8CGZ: Tubulin-AB8939 complex

tubulin-AB8939 complex. Determined by X-ray diffraction at 2.53 Å resolution. Released 14 Aug 2024.

Method: X-ray diffraction
Resolution: 2.53 Å
Organisms: Ovis aries, Rattus norvegicus
Chains: 5
Atoms: 14,545
Mol. weight: 220.21 kDa
Ligands: UIY, GDP, MG, GTP
Released: 14 Aug 2024

Explore 8CGZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CGZ contains 115 α-helices and 76 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: 29 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-28	19
α-helix	47-51	5
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	111-113	3
α-helix	115-127	13
β-strand	134-140	7	1
α-helix	144-160	17
β-strand	165-172	8	1
α-helix	175-177	3
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	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	325-338	14
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	415-435	21

Chain B: 28 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	5
α-helix	10-27	18
β-strand	30	1	6
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	103-108	6
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	285-287	3
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, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	10
α-helix	10-28	19
β-strand	35	1	11
α-helix	48-51	4
β-strand	53-55	3	12
β-strand	60	1	11
β-strand	61-63	3	12
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	115-127	13
β-strand	134-140	7	10
α-helix	144-160	17
β-strand	165-172	8	10
α-helix	175-177	3
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	13
α-helix	252-259	8
β-strand	262	1	14
β-strand	265	1	14
α-helix	268	1
β-strand	269-273	5	13
β-strand	277	1	15
α-helix	284-287	4
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	13
α-helix	307-309	3
β-strand	312-321	10	13
α-helix	325-336	12
α-helix	342	1
β-strand	343	1	13
α-helix	344	1
β-strand	351-356	6	13
α-helix	359-361	3
β-strand	368	1	15
α-helix	369-370	2
β-strand	373-381	9	13
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	415-436	22

Chain D: 28 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	16
α-helix	10-27	18
β-strand	30	1	17
β-strand	35	1	18
β-strand	36	1	17
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-56	4	18
β-strand	60-63	4	18
β-strand	65-69	5	16
α-helix	72-80	9
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	16
α-helix	103-108	6
α-helix	110-127	18
β-strand	132-140	9	16
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	16
α-helix	173	1
α-helix	183-197	15
β-strand	200-205	6	16
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	16
β-strand	269-273	5	19
α-helix	285-287	3
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	19
α-helix	307-309	3
β-strand	312-320	9	19
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	19
β-strand	351-356	6	19
α-helix	359-360	2
β-strand	374-381	8	19
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	8-14	7	3
β-strand	17-25	9	3
α-helix	49-139	91

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

>8CGZ_1 Tubulin alpha chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D), FASTA

>8CGZ_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (E), FASTA

>8CGZ_3 Stathmin-4 (chains E)
XADMEVIELNKATSGQSWEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRK
YQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLER
LQEKDKHAEEVRKNKELKEEASR

Ligands and cofactors

ID	Name	Formula	Copies
UIY	AB-8939	C22 H24 N4 O3	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
MG	Magnesium ion	Mg	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

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

Primary citation

Development of AB8939, a Novel Colchicine-like Microtubule Synthetic Destabilizer with the Ability to Overcome Multidrug Resistance. Humbert, M., Letard, S., Neves, M. et al. To be published.

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

6TH4 2.12 Å, Tubulin-inhibitor complex
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
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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