4EB6: Tubulin-Vinblastine: Stathmin-like complex

Tubulin-Vinblastine: Stathmin-like complex. Determined by X-ray diffraction at 3.47 Å resolution. Released 1 Aug 2012.

Method: X-ray diffraction
Resolution: 3.47 Å
Organisms: Ovis aries, Rattus norvegicus
Chains: 5
Atoms: 14,918
Mol. weight: 220.49 kDa
Ligands: VLB, GDP, MG, GTP
Released: 1 Aug 2012

Explore 4EB6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4EB6 contains 88 α-helices and 75 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: 20 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	1
α-helix	10-20	11
α-helix	22-24	3
α-helix	49-51	3
β-strand	53-55	3	2
β-strand	61-63	3	2
β-strand	65-69	5	1
α-helix	73-80	8
β-strand	92-94	3	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	112-126	15
β-strand	134-140	7	1
α-helix	149-160	12
β-strand	165-172	8	1
α-helix	183-194	12
β-strand	200-205	6	1
α-helix	206-210	5
α-helix	224-238	15
α-helix	240-243	4
α-helix	268	1
β-strand	269-273	5	3
β-strand	277	1	4
β-strand	301	1	3
α-helix	311	1
β-strand	312-321	10	3
α-helix	325-336	12
β-strand	343	1	3
β-strand	350-356	7	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	405-410	6
α-helix	416-434	19

Chain B: 23 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	5
α-helix	10-28	19
β-strand	30	1	6
β-strand	36	1	6
α-helix	49-51	3
β-strand	53-55	3	7
β-strand	61-63	3	7
β-strand	65-69	5	5
α-helix	72-74	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	165-171	7	5
α-helix	183-197	15
β-strand	200-203	4	5
α-helix	206-211	6
α-helix	225-238	14
α-helix	252-259	8
β-strand	267-268	2	5
β-strand	269-273	5	8
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	8
α-helix	307-309	3
β-strand	312-320	9	8
α-helix	325-330	6
α-helix	332-338	7
α-helix	340-342	3
β-strand	343	1	8
β-strand	351-356	6	8
β-strand	374-381	8	8
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-436	22

Chain C: 19 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	9
α-helix	10-26	17
α-helix	49-51	3
β-strand	53	1	10
β-strand	63	1	10
β-strand	65-69	5	9
α-helix	73-80	8
β-strand	92-94	3	9
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-121	11
α-helix	123-126	4
β-strand	134-140	7	9
α-helix	144-160	17
β-strand	165-172	8	9
α-helix	183-192	10
β-strand	200-205	6	9
α-helix	206-215	10
α-helix	224-239	16
α-helix	252-259	8
β-strand	262	1	11
β-strand	265	1	11
β-strand	271-273	3	12
β-strand	277	1	13
α-helix	288-294	7
β-strand	301	1	12
β-strand	312	1	14
β-strand	316-321	6	12
α-helix	325-338	14
β-strand	343	1	14
β-strand	352-356	5	12
β-strand	368	1	13
α-helix	369-370	2
β-strand	373-377	5	12
β-strand	381	1	14
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-410	6
α-helix	416-434	19

Chain D: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	15
α-helix	10-28	19
β-strand	30	1	16
β-strand	35	1	17
β-strand	36	1	16
α-helix	49-51	3
β-strand	53-55	3	18
β-strand	60	1	17
β-strand	61-63	3	18
β-strand	65-68	4	15
α-helix	72-75	4
α-helix	84-86	3
β-strand	93	1	15
α-helix	103-104	2
α-helix	105-109	5
α-helix	110-118	9
β-strand	134-140	7	15
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-171	7	15
α-helix	175-177	3
α-helix	183-197	15
β-strand	200-203	4	15
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-239	16
α-helix	252-259	8
β-strand	267-268	2	15
β-strand	269-273	5	19
α-helix	288-292	5
α-helix	293-295	3
α-helix	298-300	3
β-strand	301	1	19
α-helix	307-309	3
β-strand	312-320	9	19
α-helix	325-337	13
α-helix	340-342	3
β-strand	343	1	19
β-strand	351-356	6	19
β-strand	374-381	8	19
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-409	5
α-helix	415-436	22

Chain E: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	3
β-strand	12-14	3	3
β-strand	17-23	7	3
α-helix	47-136	90

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha chain	A, C	protein	451	Ovis aries	D0VWZ0 (AlphaFold model)
Tubulin beta chain	B, D	protein	445	Ovis aries	D0VWY9 (AlphaFold model)
Stathmin-4	E	protein	142	Rattus norvegicus	P63043 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4EB6_1 Tubulin alpha chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D), FASTA

>4EB6_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYSIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVATIFRGRMSMKEVDEQMLNIQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (E), FASTA

>4EB6_3 Stathmin-4 (chains E)
ADMEVIELNKATSGQSWEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRKY
QEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERL
QEKDKHAEEVRKNKELKEEASR

Ligands and cofactors

ID	Name	Formula	Copies
VLB	(2ALPHA,2'BETA,3BETA,4ALPHA,5BETA)-vincaleukoblastine	C46 H58 N4 O9	1
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

Structural plasticity of tubulin assembly probed by vinca-domain ligands. Ranaivoson, F.M., Gigant, B., Berritt, S. et al. Acta Crystallogr D Biol Crystallogr (2012) 68:927-934. DOI 10.1107/S0907444912017143 · PubMed

Other PDB entries of the same protein (UniProt D0VWZ0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EYP 1.9 Å, Tubulin-darpin complex
3RYC 2.1 Å, Tubulin: RB3 stathmin-like domain complex
9F07 2.21 Å, Tubulin:stathmin:darpin:tau MTBR3 complex
4DRX 2.22 Å, GTP-Tubulin in complex with a DARPIN
6TDE 2.29 Å, Tubulin-inhibitor complex
3RYI 2.4 Å, GDP-Tubulin: rb3 stathmin-like domain complex
5KX5 2.5 Å, Crystal structure of tubulin-stathmin-TTL-Compound 11 complex
3RYF 2.52 Å, GTP-Tubulin: RB3 Stathmin-like domain complex
4F6R 2.64 Å, Tubulin:Stathmin-like domain complex
6GVN 2.69 Å, Tubulin:TM-3 DARPin complex
3UT5 2.73 Å, Tubulin-Colchicine-Ustiloxin: Stathmin-like domain complex
6H9B 2.75 Å, 1,1-Diheterocyclic Ethylenes Derived from Quinaldine and Carbazole as New Tubulin…

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