3UT5: Tubulin alpha chain

Tubulin-Colchicine-Ustiloxin: Stathmin-like domain complex. Determined by X-ray diffraction at 2.73 Å resolution. Released 1 Aug 2012.

Method: X-ray diffraction
Resolution: 2.73 Å
Organisms: Ovis aries, Rattus norvegicus
Chains: 6
Atoms: 15,107
Mol. weight: 220.99 kDa
Ligands: GTP, MG, GDP, LOC
Released: 1 Aug 2012

Explore 3UT5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3UT5 contains 102 α-helices and 79 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: 27 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-27	18
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	111-113	3
α-helix	115-127	13
β-strand	134-140	7	1
α-helix	144-160	17
β-strand	165-172	8	1
β-strand	174	1	3
β-strand	177	1	3
α-helix	183-194	12
β-strand	200-205	6	1
α-helix	206-215	10
α-helix	224-243	20
α-helix	252-259	8
β-strand	269-273	5	4
β-strand	277	1	5
α-helix	283-285	3
α-helix	290-293	4
α-helix	294-296	3
α-helix	298-300	3
β-strand	301	1	4
β-strand	312-321	10	4
α-helix	325-336	12
α-helix	342	1
β-strand	343	1	4
α-helix	344	1
α-helix	348	1
β-strand	349-356	8	4
β-strand	368	1	5
α-helix	369-370	2
β-strand	373-381	9	4
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-409	5
α-helix	415-436	22
α-helix	438-439	2

Chain B: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	6
α-helix	10-27	18
β-strand	30	1	7
β-strand	36	1	7
α-helix	41-43	3
α-helix	49-51	3
β-strand	53-56	4	8
β-strand	60-63	4	8
β-strand	65-69	5	6
α-helix	73-80	8
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	9
β-strand	177	1	9
α-helix	183-197	15
β-strand	200-205	6	6
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-243	20
α-helix	252-259	8
β-strand	267-268	2	6
β-strand	269-273	5	10
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	10
α-helix	307-309	3
β-strand	312-321	10	10
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	10
β-strand	351-356	6	10
β-strand	373-381	9	10
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-437	23

Chain C: 26 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	11
α-helix	10-27	18
α-helix	48-51	4
β-strand	53-55	3	12
β-strand	61-63	3	12
β-strand	65-69	5	11
α-helix	73-80	8
β-strand	84	1	13
β-strand	87	1	13
α-helix	89-91	3
β-strand	92-94	3	11
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	11
α-helix	144	1
α-helix	145-149	5
α-helix	150-161	12
β-strand	165-172	8	11
α-helix	183-194	12
β-strand	200-205	6	11
α-helix	206-215	10
α-helix	224-243	20
α-helix	249-251	3
α-helix	252-259	8
β-strand	269-273	5	14
β-strand	277	1	15
α-helix	282-284	3
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	14
β-strand	312-321	10	14
α-helix	325-332	8
α-helix	335-338	4
β-strand	343	1	14
β-strand	352-356	5	14
β-strand	368	1	15
α-helix	369-370	2
β-strand	373-381	9	14
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-409	5
α-helix	415-434	20

Chain D: 24 helices, 21 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	53-55	3	19
β-strand	60	1	18
β-strand	61-63	3	19
β-strand	65-69	5	16
α-helix	73-80	8
α-helix	89-91	3
β-strand	92-94	3	16
α-helix	103-107	5
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
β-strand	174	1	20
β-strand	177	1	20
α-helix	183-197	15
β-strand	200-205	6	16
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-243	20
α-helix	252-259	8
β-strand	267-268	2	16
β-strand	269-273	5	21
α-helix	288-293	6
α-helix	298-300	3
β-strand	301	1	21
α-helix	307-309	3
β-strand	312-321	10	21
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	21
β-strand	351-356	6	21
β-strand	373-381	9	21
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-437	23

Chain E: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	4
β-strand	13-14	2	4
β-strand	17-25	9	4
α-helix	47-137	91

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)
Vinca tetrapeptide	F	protein	4

Sequence of entity 1 (A, C), FASTA

>3UT5_1 Tubulin alpha chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D), FASTA

>3UT5_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYSIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVATIFRGRMSMKEVDEQMLNIQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (E), FASTA

>3UT5_3 Stathmin-4 (chains E)
ADMEVIELNKATSGQSWEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRKY
QEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERL
QEKDKHAEEVRKNKELKEEASR

Sequence of entity 4 (F), FASTA

>3UT5_4 Vinca tetrapeptide (chains F)
YVTG

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
LOC	N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethana…	C22 H25 N O6	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
6H9B 2.75 Å, 1,1-Diheterocyclic Ethylenes Derived from Quinaldine and Carbazole as New Tubulin…
3RYH 2.8 Å, GMPCPP-Tubulin: RB3 Stathmin-like domain complex

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