8WMO: Detyrosinated tubulin alpha-1B chain
Crystal structure analysis of tubulin and heterocyclic podophyllotoxins complex for anticancer agents. Determined by X-ray diffraction at 2.89 Å resolution. Released 9 Oct 2024.
- Method
- X-ray diffraction
- Resolution
- 2.89 Å
- Organisms
- Sus scrofa, Rattus norvegicus, Gallus gallus
- Chains
- 6
- Atoms
- 16,707
- Mol. weight
- 262.14 kDa
- Ligands
- GDP, MG, GTP, ACP
- Released
- 9 Oct 2024
Explore 8WMO in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8WMO contains 120 α-helices and 94 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: 24 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-9 | 7 | 1 |
| α-helix | 10-28 | 19 | |
| 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 | 75-79 | 5 | |
| 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 | 115-127 | 13 | |
| β-strand | 132-140 | 9 | 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 | 269-271 | 3 | 4 |
| β-strand | 277 | 1 | 5 |
| 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 | 351-356 | 6 | 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 | 415-435 | 21 | |
Chain B: 25 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-9 | 7 | 6 |
| α-helix | 11-27 | 17 | |
| β-strand | 30 | 1 | 7 |
| β-strand | 36 | 1 | 7 |
| α-helix | 47-49 | 3 | |
| β-strand | 51-53 | 3 | 8 |
| β-strand | 59-61 | 3 | 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 | 101-102 | 2 | |
| α-helix | 103-107 | 5 | |
| α-helix | 108-125 | 18 | |
| β-strand | 130-138 | 9 | 6 |
| α-helix | 143-148 | 6 | |
| α-helix | 149-158 | 10 | |
| 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 | 204-212 | 9 | |
| α-helix | 222-241 | 20 | |
| α-helix | 250-257 | 8 | |
| β-strand | 265-266 | 2 | 6 |
| β-strand | 267-271 | 5 | 10 |
| α-helix | 286-294 | 9 | |
| α-helix | 296-298 | 3 | |
| β-strand | 299 | 1 | 10 |
| α-helix | 305-307 | 3 | |
| β-strand | 310-319 | 10 | 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 | 363-371 | 9 | 10 |
| α-helix | 372-374 | 3 | |
| α-helix | 375-390 | 16 | |
| α-helix | 396-399 | 4 | |
| α-helix | 405-426 | 22 | |
Chain C: 28 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-9 | 6 | 11 |
| α-helix | 10-28 | 19 | |
| β-strand | 35 | 1 | 12 |
| α-helix | 48-51 | 4 | |
| β-strand | 53-55 | 3 | 13 |
| β-strand | 60 | 1 | 12 |
| β-strand | 61-63 | 3 | 13 |
| β-strand | 65-69 | 5 | 11 |
| α-helix | 75-79 | 5 | |
| 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 | 150-160 | 11 | |
| β-strand | 165-172 | 8 | 11 |
| α-helix | 175-177 | 3 | |
| 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 | |
| β-strand | 269-273 | 5 | 14 |
| α-helix | 278-281 | 4 | |
| α-helix | 285-287 | 3 | |
| α-helix | 288-295 | 8 | |
| α-helix | 298-300 | 3 | |
| β-strand | 301 | 1 | 14 |
| α-helix | 307-309 | 3 | |
| β-strand | 312-321 | 10 | 14 |
| α-helix | 325-338 | 14 | |
| β-strand | 343 | 1 | 14 |
| β-strand | 352-356 | 5 | 14 |
| 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 | 415-435 | 21 | |
Chain D: 26 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-9 | 8 | 15 |
| α-helix | 11-27 | 17 | |
| β-strand | 30 | 1 | 16 |
| β-strand | 35 | 1 | 17 |
| β-strand | 36 | 1 | 16 |
| α-helix | 41-43 | 3 | |
| α-helix | 47-49 | 3 | |
| β-strand | 51-53 | 3 | 18 |
| β-strand | 58 | 1 | 17 |
| β-strand | 59-61 | 3 | 18 |
| β-strand | 63-67 | 5 | 15 |
| α-helix | 71-78 | 8 | |
| α-helix | 82-84 | 3 | |
| α-helix | 87-89 | 3 | |
| β-strand | 90-92 | 3 | 15 |
| α-helix | 101-102 | 2 | |
| α-helix | 103-107 | 5 | |
| α-helix | 108-125 | 18 | |
| β-strand | 129-138 | 10 | 15 |
| α-helix | 143-148 | 6 | |
| α-helix | 149-158 | 10 | |
| β-strand | 163-170 | 8 | 15 |
| α-helix | 171 | 1 | |
| α-helix | 173-175 | 3 | |
| α-helix | 181-195 | 15 | |
| β-strand | 198-203 | 6 | 15 |
| α-helix | 204-212 | 9 | |
| α-helix | 222-241 | 20 | |
| α-helix | 250-257 | 8 | |
| β-strand | 265-266 | 2 | 15 |
| β-strand | 267-271 | 5 | 19 |
| α-helix | 286-294 | 9 | |
| α-helix | 296-298 | 3 | |
| β-strand | 299 | 1 | 19 |
| α-helix | 305-307 | 3 | |
| β-strand | 310-319 | 10 | 19 |
| α-helix | 323-336 | 14 | |
| α-helix | 338-340 | 3 | |
| β-strand | 341 | 1 | 19 |
| β-strand | 349-354 | 6 | 19 |
| α-helix | 356-358 | 3 | |
| β-strand | 363-371 | 9 | 19 |
| α-helix | 374-389 | 16 | |
| α-helix | 396-399 | 4 | |
| α-helix | 405-426 | 22 | |
Chain E: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-14 | 7 | 4 |
| β-strand | 17-22 | 6 | 4 |
| α-helix | 47-137 | 91 | |
Chain F: 16 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 20 |
| α-helix | 12-22 | 11 | |
| β-strand | 27-29 | 3 | 20 |
| α-helix | 30-31 | 2 | |
| β-strand | 39-41 | 3 | 20 |
| α-helix | 49-51 | 3 | |
| β-strand | 61-62 | 2 | 20 |
| α-helix | 69-72 | 4 | |
| α-helix | 74-83 | 10 | |
| α-helix | 85-87 | 3 | |
| β-strand | 97-100 | 4 | 21 |
| α-helix | 128-139 | 12 | |
| β-strand | 147-148 | 2 | 21 |
| β-strand | 163 | 1 | 21 |
| β-strand | 180-184 | 5 | 21 |
| β-strand | 189 | 1 | 22 |
| β-strand | 192 | 1 | 23 |
| β-strand | 197 | 1 | 23 |
| β-strand | 199-207 | 9 | 24 |
| β-strand | 213-216 | 4 | 24 |
| β-strand | 220-223 | 4 | 24 |
| α-helix | 243-246 | 4 | |
| α-helix | 258-260 | 3 | |
| β-strand | 261-262 | 2 | 24 |
| α-helix | 264-275 | 12 | |
| α-helix | 279 | 1 | |
| α-helix | 280-284 | 5 | |
| α-helix | 285-298 | 14 | |
| α-helix | 299-301 | 3 | |
| β-strand | 310-311 | 2 | 20 |
| β-strand | 313-321 | 9 | 24 |
| β-strand | 322 | 1 | 22 |
| β-strand | 327-333 | 7 | 24 |
| α-helix | 340-349 | 10 | |
| α-helix | 350-355 | 6 | |
| β-strand | 375-377 | 3 | 24 |
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 | 445 | Sus scrofa | A0A8D1UIR5 (AlphaFold model) |
| Stathmin-4 | E | protein | 138 | Rattus norvegicus | P63043 (AlphaFold model) |
| Tubulin--tyrosine ligase | F | protein | 381 | Gallus gallus | A0A8C9FGJ1 (AlphaFold model) |
Sequence of entity 1 (A, C), FASTA
>8WMO_1 Detyrosinated tubulin alpha-1B chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSV
Sequence of entity 2 (B, D), FASTA
>8WMO_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA
Sequence of entity 3 (E), FASTA
>8WMO_3 Stathmin-4 (chains E)
MEVIELNKCTSGQSFEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRKYQE
AELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQE
KDKHAEEVRKNKELKEEA
Sequence of entity 4 (F), FASTA
>8WMO_4 Tubulin--tyrosine ligase (chains F)
MYTFVVRDENSSVYAEVSRLLLATGQWKRLRKDNPRFNLMLGERNRLPFGRLGHEPGLVQ
LVNYYRGADKLCRKASLVKLIKTSPELSESCTWFPESYVIYPTNLKTPVAPAQNGIRHLI
NNTRTDEREVFLAAYNRRREGREGNVWIAKSSAGAKGEGILISSEASELLDFIDEQGQVH
VIQKYLEKPLLLEPGHRKFDIRSWVLVDHLYNIYLYREGVLRTSSEPYNSANFQDKTCHL
TNHCIQKEYSKNYGRYEEGNEMFFEEFNQYLMDALNTTLENSILLQIKHIIRSCLMCIEP
AISTKHLHYQSFQLFGFDFMVDEELKVWLIEVNGAPACAQKLYAELCQGIVDVAISSVFP
LADTGQKTSQPTSIFIKLHHH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GDP | Guanosine-5'-diphosphate | C10 H15 N5 O11 P2 | 1 |
| MG | Magnesium ion | Mg | 4 |
| GTP | Guanosine-5'-triphosphate | C10 H16 N5 O14 P3 | 3 |
| ACP | Phosphomethylphosphonic acid adenylate ester | C11 H18 N5 O12 P3 | 1 |
| CA | Calcium ion | Ca | 1 |
| WIW | (5~{S},5~{a}~{R},8~{a}~{R},9~{R})-5-pyrimidin-2-ylsulfanyl-9-(3,4,5-trimethoxyp… | C26 H24 N2 O7 S | 1 |
Water and common crystallization additives (EDO, PEG, MES) are not listed.
Primary citation
Crystal structure analysis of tubulin and heterocyclic podophyllotoxins complex for anticancer agents. Zhao, W. 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
Browse structure collections
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