5JCB: Tubulin alpha-1B chain

Microtubule depolymerizing agent podophyllotoxin derivative YJTSF1. Determined by X-ray diffraction at 2.3 Å resolution. Released 27 Sept 2017.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Sus scrofa, Gallus gallus
Chains: 6
Atoms: 18,114
Mol. weight: 268.27 kDa
Ligands: MG, CA, GDP, NV4
Released: 27 Sept 2017

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

Secondary structure: helices and β-sheets

5JCB contains 130 α-helices and 98 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: 29 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-27	18
β-strand	35	1	2
α-helix	48-51	4
β-strand	53-55	3	3
β-strand	60	1	2
β-strand	61-63	3	3
β-strand	65-69	5	1
α-helix	72-79	8
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	110-126	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
β-strand	174	1	4
β-strand	177	1	4
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
β-strand	269-273	5	5
β-strand	277	1	6
α-helix	284-287	4
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	5
α-helix	307-309	3
β-strand	312-321	10	5
α-helix	325-338	14
α-helix	342	1
β-strand	343	1	5
α-helix	344	1
β-strand	349-356	8	5
α-helix	359-361	3
β-strand	368	1	6
α-helix	369-370	2
β-strand	373-381	9	5
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	416-436	21

Chain B: 26 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	7
α-helix	10-27	18
β-strand	30	1	8
β-strand	35	1	9
β-strand	36	1	8
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-54	2	10
β-strand	60	1	9
β-strand	62-63	2	10
β-strand	65-69	5	7
α-helix	73-80	8
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	7
α-helix	103-107	5
α-helix	110-127	18
β-strand	132-140	9	7
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	7
α-helix	175-177	3
α-helix	183-197	15
β-strand	200-205	6	7
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	7
β-strand	269-273	5	11
α-helix	285-287	3
α-helix	288-296	9
α-helix	298-300	3
β-strand	301	1	11
α-helix	307-309	3
β-strand	312-321	10	11
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	11
β-strand	351-356	6	11
β-strand	373-381	9	11
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-436	22

Chain C: 33 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	12
α-helix	10-28	19
β-strand	35	1	13
α-helix	48-51	4
β-strand	53-55	3	14
β-strand	60	1	13
β-strand	61-63	3	14
β-strand	65-69	5	12
α-helix	73-79	7
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	12
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	12
α-helix	144	1
α-helix	145-149	5
α-helix	150-161	12
β-strand	165-172	8	12
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	12
α-helix	206-217	12
α-helix	224-243	20
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	15
α-helix	278-281	4
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	15
α-helix	307-309	3
β-strand	312-321	10	15
α-helix	325-338	14
α-helix	342	1
β-strand	343	1	15
α-helix	344	1
α-helix	350-351	2
β-strand	352-356	5	15
α-helix	359-360	2
α-helix	369-370	2
β-strand	373-381	9	15
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 D: 27 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	16
α-helix	10-28	19
β-strand	30	1	17
β-strand	35	1	18
β-strand	36	1	17
α-helix	41-45	3
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	72-80	9
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	16
α-helix	103-107	5
α-helix	112-127	16
β-strand	134-140	7	16
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	16
α-helix	173	1
α-helix	175-177	3
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	20
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	20
α-helix	307-309	3
β-strand	312-321	10	20
α-helix	325-337	13
α-helix	340-342	3
β-strand	343	1	20
β-strand	351-356	6	20
α-helix	359-360	2
β-strand	373-381	9	20
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	5
β-strand	17-25	9	5
α-helix	47-138	92

Chain F: 14 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	21
α-helix	12-22	11
β-strand	27-29	3	21
β-strand	39-41	3	21
α-helix	49-51	3
β-strand	61-62	2	21
α-helix	69-72	4
α-helix	74-83	10
β-strand	84	1	22
β-strand	87	1	22
β-strand	97	1	23
α-helix	128-135	8
β-strand	147-150	4	23
β-strand	163	1	23
α-helix	166-170	5
β-strand	181-184	4	23
β-strand	189	1	24
β-strand	192	1	25
β-strand	197	1	25
β-strand	199-207	9	26
β-strand	213-216	4	26
β-strand	220-223	4	26
α-helix	243-246	4
β-strand	261-263	3	26
α-helix	264-275	12
α-helix	279	1
α-helix	280-284	5
α-helix	285-302	18
β-strand	310-311	2	21
β-strand	313-321	9	26
β-strand	322	1	24
β-strand	327-333	7	26
α-helix	340-342	3
α-helix	343-350	8
α-helix	351-355	5
β-strand	375-377	3	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A, C	protein	451	Sus scrofa	Q2XVP4 (AlphaFold model)
Tubulin beta chain	B, D	protein	445	Sus scrofa	A0A8D1UIR5 (AlphaFold model)
Stathmin	E	protein	152	Sus scrofa	A0A4X1VCH4 (AlphaFold model)
Tubulin-Tyrosine Ligase	F	protein	388	Gallus gallus	A0A8V0Z8P0 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5JCB_1 Tubulin alpha-1B chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D), FASTA

>5JCB_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (E), FASTA

>5JCB_3 Stathmin (chains E)
ADMEVIELNKCTSGQSFEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRKY
QEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERL
QEKDKHAEEVRKNKELKEEASRLEHHHHHHHH

Sequence of entity 4 (F), FASTA

>5JCB_4 Tubulin-Tyrosine Ligase (chains F)
MYTFVVRDENSSVYAEVSRLLLATGQWKRLRKDNPRFNLMLGERNRLPFGRLGHEPGLVQ
LVNYYRGADKLCRKASLVKLIKTSPELSESCTWFPESYVIYPTNLKTPVAPAQNGIRHLI
NNTRTDEREVFLAAYNRRREGREGNVWIAKSSAGAKGEGILISSEASELLDFIDEQGQVH
VIQKYLEKPLLLEPGHRKFDIRSWVLVDHLYNIYLYREGVLRTSSEPYNSANFQDKTCHL
TNHCIQKEYSKNYGRYEEGNEMFFEEFNQYLMDALNTTLENSILLQIKHIIRSCLMCIEP
AISTKHLHYQSFQLFGFDFMVDEELKVWLIEVNGAPACAQKLYAELCQGIVDVAISSVFP
LADTGQKTSQPTSIFIKLLEHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	7
CA	Calcium ion	Ca	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
NV4	(5R,5aR,8aS,9R)-9-[(4H-1,2,4-triazol-3-yl)sulfanyl]-5-(3,4,5-trimethoxyphenyl)-…	C24 H23 N3 O7 S	2
ACP	Phosphomethylphosphonic acid adenylate ester	C11 H18 N5 O12 P3	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

Water and common crystallization additives (IMD, MES, GOL, PEG, NA) are not listed.

Primary citation

Structural Insights into the Inhibition of Tubulin by the Antitumor Agent 4 beta-(1,2,4-triazol-3-ylthio)-4-deoxypodophyllotoxin. Zhao, W., Zhou, C., Guan, Z.Y. et al. ACS Chem Biol (2017) 12:746-752. DOI 10.1021/acschembio.6b00842 · PubMed

Other PDB entries of the same protein (UniProt Q2XVP4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9U6A 1.92 Å, Tubulin-DARPin D1 in complex with a flavone
5EZY 2.05 Å, Crystal structure of T2R-TTL-taccalonolide AJ complex
5YL2 2.09 Å, Crystal structure of T2R-TTL-Y28 complex
7TTF 2.1 Å, Tubulin-RB3_SLD in complex with compound 12k
5XKG 2.2 Å, Crystal structure of T2R-TTL-CH1 complex
7L05 2.21 Å, Complex of novel maytansinoid M24 bound to T2R-TTL (two tubulin alpha/beta heterodimers,…
9M1M 2.21 Å, Cryo-EM structure of the TBC-DEC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
5JQG 2.24 Å, An apo tubulin-RB-TTL complex structure used for side-by-side comparison
9M1N 2.24 Å, Cryo-EM structure of the TBC-DC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
5XKH 2.25 Å, Crystal structure of T2R-TTL-CF1 complex
7TTD 2.27 Å, Tubulin-RB3_SLD in complex with compound 12e
5XP3 2.3 Å, Crystal structure of apo T2R-TTL

Browse structure collections

About this viewer

MolViewer shows 5JCB directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.