9LNX: T2R-TTL-YQVB9 Complex

Crystal structure of T2R-TTL-YQVB9 Complex. Determined by X-ray diffraction at 2.59 Å resolution. Released 7 May 2025.

Method: X-ray diffraction
Resolution: 2.59 Å
Organisms: Sus scrofa, Mus musculus, Gallus gallus
Chains: 6
Atoms: 17,557
Mol. weight: 264.21 kDa
Ligands: GDP, A1EPT, CA, MG
Released: 7 May 2025

Explore 9LNX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9LNX contains 127 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: 27 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-27	18
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	72-80	9
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
α-helix	173	1
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	1
α-helix	206-217	12
α-helix	224-243	20
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	4
β-strand	277	1	5
α-helix	285-287	3
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	4
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	382-385	4
α-helix	386-399	14
α-helix	405-409	5
α-helix	415-435	21

Chain B: 27 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	19
α-helix	10-28	19
β-strand	30	1	20
β-strand	35	1	21
β-strand	36	1	20
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-56	4	21
β-strand	60-63	4	21
β-strand	65-69	5	19
α-helix	75-79	5
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	19
α-helix	103-107	5
α-helix	110-127	18
β-strand	132-140	9	19
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	19
α-helix	173	1
α-helix	183-197	15
β-strand	200-205	6	19
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	19
β-strand	269-273	5	22
α-helix	285-287	3
α-helix	288-296	9
α-helix	298-300	3
β-strand	301	1	22
α-helix	307-309	3
β-strand	312-320	9	22
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	22
β-strand	351-356	6	22
α-helix	359-360	2
β-strand	374-381	8	22
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	6
α-helix	10-28	19
β-strand	35	1	7
α-helix	49-51	3
β-strand	53-55	3	8
β-strand	60	1	7
β-strand	61-63	3	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	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-126	12
β-strand	134-140	7	6
α-helix	144	1
α-helix	145-149	5
α-helix	150-161	12
β-strand	165-172	8	6
α-helix	173	1
α-helix	175-177	3
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	6
α-helix	206-216	11
α-helix	224-243	20
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	9
α-helix	278-281	4
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	9
α-helix	307-309	3
β-strand	312-321	10	9
α-helix	325-336	12
β-strand	343	1	9
β-strand	351-356	6	9
α-helix	359-360	2
α-helix	369-370	2
β-strand	373-381	9	9
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	10
α-helix	10-28	19
β-strand	30	1	11
β-strand	36	1	11
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-56	4	12
β-strand	60-63	4	12
β-strand	65-69	5	10
α-helix	74-80	7
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	10
α-helix	103-108	6
α-helix	110-127	18
β-strand	132-140	9	10
α-helix	145-160	16
β-strand	165-172	8	10
α-helix	173	1
α-helix	183-197	15
β-strand	200-205	6	10
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-238	15
α-helix	240-243	4
α-helix	252-259	8
β-strand	267-268	2	10
β-strand	269-273	5	13
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	340-342	3
β-strand	343	1	13
β-strand	351-356	6	13
β-strand	373-381	9	13
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-410	5
α-helix	416-436	21

Chain E: 1 helix, 2 β-strands

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

Chain F: 16 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	14
α-helix	12-22	11
β-strand	27-29	3	14
β-strand	39-41	3	14
α-helix	49-51	3
β-strand	61-62	2	14
α-helix	68-71	4
α-helix	74-83	10
β-strand	97-100	4	15
α-helix	129-135	7
β-strand	147-148	2	15
β-strand	163	1	15
α-helix	166-173	8
β-strand	180-184	5	15
β-strand	189	1	16
β-strand	192	1	17
β-strand	197	1	17
β-strand	199-207	9	18
β-strand	213-216	4	18
β-strand	220-223	4	18
α-helix	227-228	2
α-helix	258-260	3
β-strand	261-263	3	18
α-helix	264-270	7
α-helix	271-275	5
α-helix	279	1
α-helix	280-284	5
α-helix	285-302	18
β-strand	310-311	2	14
β-strand	313-321	9	18
β-strand	322	1	16
β-strand	327-333	7	18
α-helix	340-342	3
α-helix	343-350	8
α-helix	351-355	5
β-strand	375-377	3	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Detyrosinated tubulin alpha-1B chain	A, C	protein	450	Sus scrofa	Q2XVP4 (AlphaFold model)
Tubulin beta chain	B, D	protein	445	Sus scrofa	A0A8D1UIR5 (AlphaFold model)
Stathmin-4	E	protein	143	Mus musculus	P63042 (AlphaFold model)
Tubulin tyrosine ligase	F	protein	384	Gallus gallus	A0A8V0Z8P0 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9LNX_1 Detyrosinated tubulin alpha-1B chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEE

Sequence of entity 2 (B, D), FASTA

>9LNX_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (E), FASTA

>9LNX_3 Stathmin-4 (chains E)
MADMEVIELNKCTSGQSFEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRK
YQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLER
LQEKDKHAEEVRKNKELKEEASR

Sequence of entity 4 (F), FASTA

>9LNX_4 Tubulin tyrosine ligase (chains F)
MYTFVVRDENSSVYAEVSRLLLATGQWKRLRKDNPRFNLMLGERNRLPFGRLGHEPGLVQ
LVNYYRGADKLCRKASLVKLIKTSPELSESCTWFPESYVIYPTNLKTPVAPAQNGIRHLI
NNTRTDEREVFLAAYNRRREGREGNVWIAKSSAGAKGEGILISSEASELLDFIDEQGQVH
VIQKYLEKPLLLEPGHRKFDIRSWVLVDHLYNIYLYREGVLRTSSEPYNSANFQDKTCHL
TNHCIQKEYSKNYGRYEEGNEMFFEEFNQYLMDALNTTLENSILLQIKHIIRSCLMCIEP
AISTKHLHYQSFQLFGFDFMVDEELKVWLIEVNGAPACAQKLYAELCQGIVDVAISSVFP
LADTGQKTSQPTSIFIKLHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
A1EPT	10'-methoxyvinblastine	C47 H60 N4 O10	1
CA	Calcium ion	Ca	2
MG	Magnesium ion	Mg	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

Primary citation

Crystal structure of T2R-TTL-YQVB9 Complex. Wu, C.Y., Wang, Y.X., Chen, Q.F. 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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