8WMU: Detyrosinated tubulin alpha-1B chain
Structural basis of tubulin and heterocyclic podophyllotoxins complex for anticancer agents with dual-binding sites. Determined by X-ray diffraction at 2.7 Å resolution. Released 9 Oct 2024.
- Method
- X-ray diffraction
- Resolution
- 2.7 Å
- Organisms
- Sus scrofa, Rattus norvegicus, Gallus gallus
- Chains
- 6
- Atoms
- 17,170
- Mol. weight
- 258.49 kDa
- Ligands
- GTP, CA, GDP, A1D55
- Released
- 9 Oct 2024
Explore 8WMU in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8WMU contains 125 α-helices and 97 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 | 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 | 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 | 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 | 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 | |
| β-strand | 269-273 | 5 | 4 |
| β-strand | 277 | 1 | 5 |
| 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 | 325-336 | 12 | |
| 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 | 385-400 | 16 | |
| α-helix | 405-409 | 5 | |
| α-helix | 415-436 | 22 | |
Chain B: 27 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-9 | 7 | 6 |
| α-helix | 10-27 | 18 | |
| β-strand | 30 | 1 | 7 |
| β-strand | 35 | 1 | 8 |
| β-strand | 36 | 1 | 7 |
| α-helix | 41-43 | 3 | |
| α-helix | 47-49 | 3 | |
| β-strand | 51-52 | 2 | 9 |
| β-strand | 58 | 1 | 8 |
| β-strand | 60-61 | 2 | 9 |
| 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 | 101-106 | 6 | |
| α-helix | 108-125 | 18 | |
| 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 | 10 |
| β-strand | 175 | 1 | 10 |
| α-helix | 181-195 | 15 | |
| β-strand | 198-203 | 6 | 6 |
| α-helix | 204-209 | 6 | |
| α-helix | 210-214 | 5 | |
| α-helix | 222-241 | 20 | |
| α-helix | 250-257 | 8 | |
| β-strand | 265-266 | 2 | 6 |
| β-strand | 267-271 | 5 | 11 |
| α-helix | 283-285 | 3 | |
| α-helix | 286-294 | 9 | |
| α-helix | 296-298 | 3 | |
| β-strand | 299 | 1 | 11 |
| α-helix | 305-307 | 3 | |
| β-strand | 310-319 | 10 | 11 |
| α-helix | 323-336 | 14 | |
| α-helix | 338-340 | 3 | |
| β-strand | 341 | 1 | 11 |
| β-strand | 349-354 | 6 | 11 |
| α-helix | 356-358 | 3 | |
| β-strand | 363-371 | 9 | 11 |
| α-helix | 372-374 | 3 | |
| α-helix | 375-389 | 15 | |
| α-helix | 396-399 | 4 | |
| α-helix | 405-427 | 23 | |
Chain C: 31 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-9 | 7 | 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 | 73-80 | 8 | |
| 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 | 115-126 | 12 | |
| β-strand | 132-140 | 9 | 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 | 249-251 | 3 | |
| α-helix | 252-259 | 8 | |
| β-strand | 269-273 | 5 | 15 |
| β-strand | 277 | 1 | 16 |
| α-helix | 278-281 | 4 | |
| α-helix | 288-294 | 7 | |
| α-helix | 298-300 | 3 | |
| β-strand | 301 | 1 | 15 |
| α-helix | 307-309 | 3 | |
| β-strand | 312-321 | 10 | 15 |
| α-helix | 325-336 | 12 | |
| β-strand | 343 | 1 | 15 |
| α-helix | 350-351 | 2 | |
| β-strand | 352-356 | 5 | 15 |
| α-helix | 359-360 | 2 | |
| β-strand | 368 | 1 | 16 |
| 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: 25 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-9 | 7 | 17 |
| α-helix | 10-27 | 18 | |
| β-strand | 30 | 1 | 18 |
| β-strand | 35 | 1 | 19 |
| β-strand | 36 | 1 | 18 |
| α-helix | 41-43 | 3 | |
| α-helix | 47-49 | 3 | |
| β-strand | 51-54 | 4 | 19 |
| β-strand | 58-61 | 4 | 19 |
| β-strand | 63-67 | 5 | 17 |
| α-helix | 70-78 | 9 | |
| α-helix | 87-89 | 3 | |
| β-strand | 90-92 | 3 | 17 |
| α-helix | 101-105 | 5 | |
| α-helix | 108-125 | 18 | |
| β-strand | 130-138 | 9 | 17 |
| α-helix | 143-147 | 5 | |
| α-helix | 148-158 | 11 | |
| β-strand | 163-170 | 8 | 17 |
| α-helix | 171 | 1 | |
| α-helix | 181-195 | 15 | |
| β-strand | 198-203 | 6 | 17 |
| α-helix | 204-209 | 6 | |
| α-helix | 210-214 | 5 | |
| α-helix | 222-241 | 20 | |
| α-helix | 250-257 | 8 | |
| β-strand | 265-266 | 2 | 17 |
| β-strand | 267-271 | 5 | 20 |
| α-helix | 286-293 | 8 | |
| α-helix | 296-298 | 3 | |
| β-strand | 299 | 1 | 20 |
| α-helix | 305-307 | 3 | |
| β-strand | 310-319 | 10 | 20 |
| α-helix | 323-335 | 13 | |
| α-helix | 338-340 | 3 | |
| β-strand | 341 | 1 | 20 |
| β-strand | 349-354 | 6 | 20 |
| α-helix | 356-358 | 3 | |
| β-strand | 363-371 | 9 | 20 |
| α-helix | 372-374 | 3 | |
| α-helix | 375-389 | 15 | |
| α-helix | 396-399 | 4 | |
| α-helix | 405-427 | 23 | |
Chain E: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-14 | 8 | 4 |
| β-strand | 17-25 | 9 | 4 |
| α-helix | 47-138 | 92 | |
Chain F: 15 helices, 20 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 | 97-99 | 3 | 22 |
| α-helix | 130-140 | 11 | |
| β-strand | 147-148 | 2 | 22 |
| β-strand | 163 | 1 | 22 |
| α-helix | 166-171 | 6 | |
| β-strand | 181-184 | 4 | 22 |
| β-strand | 189 | 1 | 23 |
| β-strand | 192 | 1 | 24 |
| β-strand | 197 | 1 | 24 |
| β-strand | 199-207 | 9 | 25 |
| β-strand | 213-216 | 4 | 25 |
| β-strand | 220-223 | 4 | 25 |
| α-helix | 227-228 | 2 | |
| α-helix | 243-246 | 4 | |
| β-strand | 261-262 | 2 | 25 |
| 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 | 25 |
| β-strand | 322 | 1 | 23 |
| β-strand | 327-333 | 7 | 25 |
| α-helix | 340-342 | 3 | |
| α-helix | 343-350 | 8 | |
| α-helix | 351-355 | 5 | |
| β-strand | 375-377 | 3 | 25 |
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 | 138 | Rattus norvegicus | P63043 (AlphaFold model) |
| Tubulin--tyrosine ligase | F | protein | 380 | Gallus gallus | A0A8C9FGJ1 (AlphaFold model) |
Sequence of entity 1 (A, C), FASTA
>8WMU_1 Detyrosinated tubulin alpha-1B chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSV
Sequence of entity 2 (B, D), FASTA
>8WMU_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAD
Sequence of entity 3 (E), FASTA
>8WMU_3 Stathmin-4 (chains E)
MEVIELNKCTSGQSFEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRKYQE
AELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQE
KDKHAEEVRKNKELKEEA
Sequence of entity 4 (F), FASTA
>8WMU_4 Tubulin--tyrosine ligase (chains F)
MYTFVVRDENSSVYAEVSRLLLATGQWKRLRKDNPRFNLMLGERNRLPFGRLGHEPGLVQ
LVNYYRGADKLCRKASLVKLIKTSPELSESCTWFPESYVIYPTNLKTPVAPAQNGIRHLI
NNTRTDEREVFLAAYNRRREGREGNVWIAKSSAGAKGEGILISSEASELLDFIDEQGQVH
VIQKYLEKPLLLEPGHRKFDIRSWVLVDHLYNIYLYREGVLRTSSEPYNSANFQDKTCHL
TNHCIQKEYSKNYGRYEEGNEMFFEEFNQYLMDALNTTLENSILLQIKHIIRSCLMCIEP
AISTKHLHYQSFQLFGFDFMVDEELKVWLIEVNGAPACAQKLYAELCQGIVDVAISSVFP
LADTGQKTSQPTSIFIKLHH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GTP | Guanosine-5'-triphosphate | C10 H16 N5 O14 P3 | 3 |
| CA | Calcium ion | Ca | 2 |
| GDP | Guanosine-5'-diphosphate | C10 H15 N5 O11 P2 | 1 |
| A1D55 | (5~{S},5~{a}~{S},8~{a}~{R},9~{R})-5-(quinolin-6-ylamino)-9-(3,4,5-trimethoxyphe… | C31 H28 N2 O7 | 1 |
| ACP | Phosphomethylphosphonic acid adenylate ester | C11 H18 N5 O12 P3 | 1 |
| MG | Magnesium ion | Mg | 3 |
Water and common crystallization additives (GOL, PEG, MES, EDO) are not listed.
Primary citation
Structural basis of tubulin and heterocyclic podophyllotoxins complex for anticancer agents with dual-binding sites. 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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