8YEM: Tubulin-RB3_SLD-TTL

Tubulin-RB3_SLD-TTL in complex with compound 9. Determined by X-ray diffraction at 2.74 Å resolution. Released 26 Feb 2025.

Method: X-ray diffraction
Resolution: 2.74 Å
Organisms: Sus scrofa, Rattus norvegicus, Gallus gallus
Chains: 6
Atoms: 17,399
Mol. weight: 258.32 kDa
Ligands: GDP, MG, CA, GTP
Released: 26 Feb 2025

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

Secondary structure: helices and β-sheets

8YEM contains 129 α-helices and 92 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: 26 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-28	19
β-strand	35	1	2
α-helix	49-51	3
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	89-91	3
β-strand	92-94	3	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	115-126	12
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	206-215	10
α-helix	224-243	20
α-helix	252-259	8
β-strand	269-273	5	4
β-strand	277	1	5
α-helix	284-287	4
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	4
α-helix	307-309	3
β-strand	312-321	10	4
α-helix	325-338	14
β-strand	343	1	4
β-strand	349-356	8	4
α-helix	359-361	3
β-strand	368	1	5
α-helix	369-370	2
β-strand	373-381	9	4
α-helix	382-384	3
α-helix	385-401	17
α-helix	405-409	5
α-helix	415-435	21

Chain B: 29 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	47-49	3
β-strand	51-54	4	8
β-strand	58-61	4	8
β-strand	63-67	5	6
α-helix	71-78	8
α-helix	82-84	3
α-helix	87-89	3
β-strand	90-92	3	6
α-helix	101-105	5
α-helix	108-126	19
β-strand	130-138	9	6
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-170	8	6
α-helix	171	1
β-strand	172	1	9
β-strand	175	1	9
α-helix	181-195	15
β-strand	198-203	6	6
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
α-helix	238-241	4
α-helix	250-257	8
β-strand	265-266	2	6
β-strand	267-271	5	10
α-helix	278-280	3
α-helix	282-285	4
α-helix	286-293	8
α-helix	296-298	3
β-strand	299	1	10
α-helix	305-307	3
β-strand	310-318	9	10
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	10
β-strand	349-354	6	10
α-helix	356-358	3
β-strand	364-371	8	10
α-helix	372-374	3
α-helix	375-389	15
α-helix	396-399	4
α-helix	405-425	21

Chain C: 33 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	11
α-helix	10-28	19
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
α-helix	84-86	3
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	115-126	12
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
α-helix	195-197	3
β-strand	200-205	6	11
α-helix	206-216	11
α-helix	224-243	20
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	13
β-strand	277	1	14
α-helix	278-281	4
α-helix	285-287	3
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	325-338	14
α-helix	342	1
β-strand	343	1	13
α-helix	344	1
α-helix	350-351	2
β-strand	352-356	5	13
α-helix	359-360	2
β-strand	368	1	14
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
α-helix	438-439	2

Chain D: 25 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	15
α-helix	10-28	19
β-strand	30	1	16
β-strand	36	1	16
α-helix	41-43	3
α-helix	47-49	3
β-strand	51-54	4	17
β-strand	58-61	4	17
β-strand	63-67	5	15
α-helix	70-78	9
α-helix	87-89	3
β-strand	90-92	3	15
α-helix	101-105	5
α-helix	108-124	17
β-strand	130-138	9	15
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-170	8	15
α-helix	181-195	15
β-strand	198-203	6	15
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-235	14
α-helix	238-241	4
α-helix	250-257	8
β-strand	265-266	2	15
β-strand	267-271	5	18
α-helix	286-293	8
α-helix	296-298	3
β-strand	299	1	18
α-helix	305-307	3
β-strand	310-319	10	18
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	18
β-strand	349-354	6	18
α-helix	357-358	2
β-strand	363-371	9	18
α-helix	372-374	3
α-helix	375-389	15
α-helix	396-399	4
α-helix	405-426	22

Chain E: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	4
β-strand	12-13	2	4
β-strand	17-25	9	4
α-helix	47-137	91

Chain F: 15 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	19
α-helix	12-22	11
β-strand	27-29	3	19
β-strand	39-41	3	19
α-helix	49-51	3
β-strand	61-62	2	19
α-helix	68-71	4
α-helix	74-83	10
β-strand	97-100	4	20
α-helix	131-141	11
β-strand	147-148	2	20
α-helix	166-174	9
β-strand	180-184	5	20
β-strand	189	1	21
β-strand	192	1	22
β-strand	197	1	22
β-strand	199-207	9	23
β-strand	213-216	4	23
β-strand	220-223	4	23
α-helix	258-260	3
β-strand	261-262	2	23
α-helix	264-275	12
α-helix	279	1
α-helix	280-284	5
α-helix	285-297	13
α-helix	299-302	4
β-strand	310-311	2	19
β-strand	313-321	9	23
β-strand	322	1	21
β-strand	327-333	7	23
α-helix	336-339	4
α-helix	340-350	11
α-helix	351-355	5
β-strand	375-377	3	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Detyrosinated tubulin alpha-1B chain	A, C	protein	440	Sus scrofa	Q2XVP4 (AlphaFold model)
Tubulin beta chain	B, D	protein	431	Sus scrofa	A0A8D1UIR5 (AlphaFold model)
Stathmin-4	E	protein	136	Rattus norvegicus	P63043 (AlphaFold model)
Tubulin--tyrosine ligase	F	protein	380	Gallus gallus	A0A8C9FGJ1 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8YEM_1 Detyrosinated tubulin alpha-1B chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSV

Sequence of entity 2 (B, D), FASTA

>8YEM_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAD

Sequence of entity 3 (E), FASTA

>8YEM_3 Stathmin-4 (chains E)
MEVIELNKCTSGQSFEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRKYQE
AELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQE
KDKHAEEVRKNKELKE

Sequence of entity 4 (F), FASTA

>8YEM_4 Tubulin--tyrosine ligase (chains F)
MYTFVVRDENSSVYAEVSRLLLATGQWKRLRKDNPRFNLMLGERNRLPFGRLGHEPGLVQ
LVNYYRGADKLCRKASLVKLIKTSPELSESCTWFPESYVIYPTNLKTPVAPAQNGIRHLI
NNTRTDEREVFLAAYNRRREGREGNVWIAKSSAGAKGEGILISSEASELLDFIDEQGQVH
VIQKYLEKPLLLEPGHRKFDIRSWVLVDHLYNIYLYREGVLRTSSEPYNSANFQDKTCHL
TNHCIQKEYSKNYGRYEEGNEMFFEEFNQYLMDALNTTLENSILLQIKHIIRSCLMCIEP
AISTKHLHYQSFQLFGFDFMVDEELKVWLIEVNGAPACAQKLYAELCQGIVDVAISSVFP
LADTGQKTSQPTSIFIKLHH

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
MG	Magnesium ion	Mg	3
CA	Calcium ion	Ca	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
ACP	Phosphomethylphosphonic acid adenylate ester	C11 H18 N5 O12 P3	1
A1D6D	4-(2-chloranyl-6-fluoranyl-quinazolin-4-yl)-7-methoxy-1,3-dihydroquinoxalin-2-o…	C17 H12 Cl F N4 O2	2

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

Primary citation

Tubulin-RB3_SLD-TTL in complex with compound 9. Wu, C.Y., Wang, Y.X. To be published.

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
5JCB 2.3 Å, Microtubule depolymerizing agent podophyllotoxin derivative YJTSF1

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