5S61: Tubulin-Z57472297-complex

Tubulin-Z57472297-complex. Determined by X-ray diffraction at 1.95 Å resolution. Released 30 Jun 2021.

Method: X-ray diffraction
Resolution: 1.95 Å
Organisms: Bos taurus, Rattus norvegicus, Gallus gallus
Chains: 6
Atoms: 18,159
Mol. weight: 265.22 kDa
Ligands: ACP, GDP, CA, MG
Released: 30 Jun 2021

Explore 5S61 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5S61 contains 129 α-helices and 91 β-strands across 6 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	73-79	7
α-helix	84-86	3
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	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	1
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	1
α-helix	206-216	11
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	283-286	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
β-strand	343	1	3
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	385-400	16
α-helix	405-409	5
α-helix	416-436	21

Chain B: 27 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	5
α-helix	10-27	18
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
α-helix	57-59	3
β-strand	60-63	4	7
β-strand	65-69	5	5
α-helix	73-79	7
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	5
α-helix	103-107	5
α-helix	110-127	18
β-strand	131-140	10	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	224-243	20
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	415-436	22

Chain C: 31 helices, 16 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	73-79	7
α-helix	84-86	3
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	1
α-helix	145-149	5
α-helix	150-161	12
β-strand	165-172	8	10
α-helix	183-195	13
β-strand	200-205	6	10
α-helix	206-216	11
α-helix	224-243	20
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	12
β-strand	277	1	13
α-helix	278-281	4
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	12
α-helix	307-309	3
β-strand	312-321	10	12
α-helix	325-338	14
α-helix	342	1
β-strand	343	1	12
α-helix	344	1
β-strand	352-356	5	12
α-helix	359-360	2
β-strand	368	1	13
α-helix	369-370	2
β-strand	373-381	9	12
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-410	6
α-helix	415-436	22
α-helix	438-439	2

Chain D: 27 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	14
α-helix	10-28	19
β-strand	30	1	15
β-strand	36	1	15
α-helix	41-45	3
α-helix	49-51	3
β-strand	53-56	4	16
β-strand	60-63	4	16
β-strand	65-69	5	14
α-helix	73-80	8
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	14
α-helix	103-107	5
α-helix	110-127	18
β-strand	134-140	7	14
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	14
α-helix	173	1
α-helix	183-197	15
β-strand	200-205	6	14
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	14
β-strand	269-273	5	17
α-helix	285-287	3
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	17
α-helix	307-309	3
β-strand	312-321	10	17
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	17
β-strand	351-356	6	17
α-helix	359-360	2
β-strand	373-381	9	17
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	47-142	96

Chain F: 15 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	18
α-helix	12-23	12
β-strand	27-30	4	18
β-strand	39-41	3	18
α-helix	49-51	3
β-strand	61-62	2	18
α-helix	69-72	4
α-helix	74-83	10
β-strand	97-100	4	19
α-helix	128-140	13
β-strand	147-150	4	19
β-strand	161-163	3	19
α-helix	166-174	9
β-strand	180-184	5	19
β-strand	189	1	20
β-strand	192	1	21
β-strand	197	1	21
β-strand	199-207	9	22
β-strand	213-216	4	22
β-strand	220-223	4	22
α-helix	243-249	7
α-helix	258-260	3
β-strand	261-263	3	22
α-helix	264-275	12
α-helix	279	1
α-helix	280-284	5
α-helix	285-302	18
β-strand	310-311	2	18
β-strand	313-321	9	22
β-strand	322	1	20
β-strand	327-333	7	22
α-helix	340-342	3
α-helix	343-350	8
α-helix	351-355	5
β-strand	375-378	4	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A, C	protein	451	Bos taurus	P81947 (AlphaFold model)
Tubulin beta-2B chain	B, D	protein	445	Bos taurus	Q6B856 (AlphaFold model)
Stathmin-4	E	protein	143	Rattus norvegicus	P63043 (AlphaFold model)
Tubulin-Tyrosine Ligase	F	protein	384	Gallus gallus	A0A8V0Z8P0 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5S61_1 Tubulin alpha-1B chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D), FASTA

>5S61_2 Tubulin beta-2B chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (E), FASTA

>5S61_3 Stathmin-4 (chains E)
MADMEVIELNKCTSGQSFEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRK
YQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLER
LQEKDKHAEEVRKNKELKEEASR

Sequence of entity 4 (F), FASTA

>5S61_4 Tubulin-Tyrosine Ligase (chains F)
MYTFVVRDENSSVYAEVSRLLLATGQWKRLRKDNPRFNLMLGERNRLPFGRLGHEPGLVQ
LVNYYRGADKLCRKASLVKLIKTSPELSESCTWFPESYVIYPTNLKTPVAPAQNGIRHLI
NNTRTDEREVFLAAYNRRREGREGNVWIAKSSAGAKGEGILISSEASELLDFIDEQGQVH
VIQKYLEKPLLLEPGHRKFDIRSWVLVDHLYNIYLYREGVLRTSSEPYNSANFQDKTCHL
TNHCIQKEYSKNYGRYEEGNEMFFEEFNQYLMDALNTTLENSILLQIKHIIRSCLMCIEP
AISTKHLHYQSFQLFGFDFMVDEELKVWLIEVNGAPACAQKLYAELCQGIVDVAISSVFP
LADTGQKTSQPTSIFIKLHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ACP	Phosphomethylphosphonic acid adenylate ester	C11 H18 N5 O12 P3	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
CA	Calcium ion	Ca	4
MG	Magnesium ion	Mg	5
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
AYV	1-[2-methyl-1,3-bis(oxidanyl)propan-2-yl]-3-phenyl-urea	C11 H16 N2 O3	3

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

Primary citation

Comprehensive Analysis of Binding Sites in Tubulin. Muhlethaler, T., Gioia, D., Prota, A.E. et al. Angew Chem Int Ed Engl (2021) 60:13331-13342. DOI 10.1002/anie.202100273 · 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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