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- PDB-6lsn: Crystal structure of tubulin-inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 6lsn
TitleCrystal structure of tubulin-inhibitor complex
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta chain
  • Tubulin tyrosine ligase
KeywordsCELL CYCLE / Inhibitor
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins ...tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / microtubule depolymerization / COPI-mediated anterograde transport / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / growth cone / microtubule / neuron projection / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm
Similarity search - Function
Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. ...Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Chem-ERR / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin tyrosine ligase / Tubulin beta chain / Stathmin-4 / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesSus scrofa (pig)
Mus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.445 Å
AuthorsGang, L. / Wang, Y.X. / Cheng, J.J.
CitationJournal: To Be Published
Title: Design, Synthesis, and Bioevaluation of Pyrazolo[1,5-a]Pyrimidine Derivatives as Tubulin Polymerization Inhibitors Targeting the Colchicine Binding Site with Potent Anticancer Activities
Authors: Gang, L. / Wang, Y.X. / Chen, J.J.
History
DepositionJan 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta chain
C: Tubulin alpha-1B chain
D: Tubulin beta chain
E: Stathmin-4
F: Tubulin tyrosine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,88925
Polymers261,3056
Non-polymers3,58419
Water6,774376
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22900 Å2
ΔGint-157 kcal/mol
Surface area81280 Å2
Unit cell
Length a, b, c (Å)105.296, 158.458, 181.959
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 6 molecules ACBDEF

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50041.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: TUBA1B / Production host: Escherichia coli (E. coli) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta chain


Mass: 49999.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: TUBB2B / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A287AGU7, UniProt: P02554*PLUS
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16844.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Stmn4 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P63042
#4: Protein Tubulin tyrosine ligase


Mass: 44378.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43

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Non-polymers , 9 types, 395 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#10: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Chemical ChemComp-ERR / 2-(1-methylindol-5-yl)-7-(3,4,5-trimethoxyphenyl)pyrazolo[1,5-a]pyrimidine


Mass: 414.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H22N4O3 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 6% PEG, 5% glycerol, 0.1M MES, 30 mM CaCl2, 30 mM MgCl2, pH 6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.445→50 Å / Num. obs: 112697 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.055 / Rrim(I) all: 0.143 / Χ2: 0.423 / Net I/σ(I): 2.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.495.91.06955560.620.4721.170.409100
2.49-2.5460.9555640.6560.4221.0410.40699.8
2.54-2.596.30.81555710.7320.350.8880.407100
2.59-2.646.40.68355770.7960.2910.7430.406100
2.64-2.76.90.65455940.8350.2670.7070.416100
2.7-2.766.80.56355660.8610.230.6090.416100
2.76-2.836.80.47855620.9050.1960.5170.423100
2.83-2.96.70.39155860.9330.1620.4240.421100
2.9-2.996.60.34356090.9380.1430.3720.432100
2.99-3.096.40.26655920.9580.1140.290.431100
3.09-3.26.40.21956050.970.0940.2390.437100
3.2-3.326.80.18456080.9820.0760.20.435100
3.32-3.486.90.1556130.9890.0610.1620.443100
3.48-3.666.90.12456590.9910.0510.1340.454100
3.66-3.896.80.09956420.9940.0410.1070.445100
3.89-4.196.40.0856500.9950.0340.0880.433100
4.19-4.616.80.06656750.9970.0270.0720.424100
4.61-5.286.90.06357220.9970.0260.0690.413100
5.28-6.656.30.06857520.9960.0290.0740.399100
6.65-506.30.04859940.9980.020.0520.40499.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I55

4i55


Resolution: 2.445→33.167 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.8
RfactorNum. reflection% reflection
Rfree0.22 2000 1.78 %
Rwork0.1766 --
obs0.1774 112322 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 178.45 Å2 / Biso mean: 61.2834 Å2 / Biso min: 17.41 Å2
Refinement stepCycle: final / Resolution: 2.445→33.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17401 0 217 376 17994
Biso mean--58.97 52.71 -
Num. residues----2200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4453-2.50640.29491380.2619757697
2.5064-2.57420.28431410.24967793100
2.5742-2.64990.26821410.22987815100
2.6499-2.73540.2571420.22347844100
2.7354-2.83310.2751430.23037868100
2.8331-2.94650.30631420.22557805100
2.9465-3.08050.26371420.20847869100
3.0805-3.24280.24981430.20587867100
3.2428-3.44570.24471430.1927903100
3.4457-3.71140.24381430.17117908100
3.7114-4.08430.19741430.14787911100
4.0843-4.6740.16551450.13297980100
4.674-5.88330.18311460.14818042100
5.8833-33.1670.17811480.1567814198
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1873-0.0180.05440.0429-0.02680.04970.00310.0879-0.0749-0.27780.1888-0.1627-0.3840.05560.03120.4994-0.1070.11060.2989-0.0910.317429.422497.834453.9046
20.0623-0.01050.03660.00650.00610.0214-0.0460.2061-0.1201-0.1680.2714-0.041-0.29480.0411-00.5727-0.10220.06960.3182-0.02470.301428.566887.81342.527
30.241-0.0628-0.01010.4336-0.08080.52240.010.0277-0.0062-0.00080.18-0.1617-0.01590.24390.40730.2177-0.04810.05010.3483-0.15980.347135.116678.730155.2357
40.0051-0.00670.00280.03340.02020.0270.1477-0.1213-0.07290.0634-0.0024-0.0315-0.1208-0.088900.29750.0425-0.00470.342-0.06990.365911.911880.23960.1192
5-0.00380.06190.02630.15860.1240.2650.0127-0.0185-0.03520.07950.0032-0.0091-0.1233-0.020400.2620.00280.04130.2315-0.06580.249318.819187.603368.5107
60.05750.00660.0070.00580.05240.0403-0.0646-0.12980.06310.16030.06970.13410.0140.0801-00.59460.0430.06160.3476-0.06970.380216.672488.114180.6973
70.13680.22920.0250.13440.10020.23540.0060.0206-0.02240.12160.027-0.00320.00970.065900.26280.03010.00710.2262-0.06090.223722.27677.049166.443
80.011-0.00670.01740.0031-0.00860.01-0.01760.0891-0.09550.29890.0182-0.11090.10110.054400.43820.1137-0.05640.4265-0.04980.395230.973164.048870.5813
90.0026-0.01220.02840.011-0.01290.01760.16970.07580.11330.03050.0712-0.0041-0.1354-0.0646-00.30050.00990.08030.2954-0.04470.385915.264564.930521.3434
100.14650.0270.01230.0163-0.00820.01040.23860.19110.1975-0.2022-0.1611-0.1312-0.23270.006100.52460.0410.11660.3461-0.00640.485915.950772.79117.4362
110.138-0.0310.10430.02290.00670.14330.27230.1277-0.1028-0.1394-0.0852-0.092-0.0940.28060.02460.2706-0.06880.10260.3552-0.06010.300628.789456.709314.3348
120.0707-0.0587-0.095-0.00620.10510.09210.0328-0.00270.1039-0.08440.02220.0664-0.04250.030800.2325-0.04020.04360.3192-0.09080.325923.904456.349825.2163
130.001-0.07680.0290.02980.04160.11270.0446-0.12350.02770.13-0.13090.03080.1271-0.077400.24420.00020.02950.33-0.10810.352215.475148.912329.0646
140.0942-0.1012-0.22130.09610.07070.20190.0905-0.08660.0540.0624-0.14290.0927-0.1116-0.1893-00.28620.00220.02460.3681-0.1240.422810.496563.16130.9965
150.0308-0.0003-0.01160.04550.0430.08870.08290.11990.0301-0.006-0.15140.00660.005-0.0528-00.21660.0273-0.00060.3226-0.11840.32195.482359.646437.253
160.04440.0041-0.00660.0151-0.00710.0996-0.0823-0.10180.00740.06220.0098-0.0722-0.0115-0.339600.32560.03110.05550.4326-0.10960.37876.353761.530344.6566
17-0.0378-0.10110.0864-0.0309-0.00480.08630.06190.0459-0.00990.0983-0.09330.1340.1668-0.1855-00.18590.0090.04410.2651-0.06130.275214.284944.021234.1131
18-0.00970.0549-0.02290.1224-0.0540.01730.04330.0149-0.08060.17460.0117-0.12240.23630.069100.21940.0211-0.0310.2985-0.04140.284125.187238.761130.9124
190.12030.0362-0.06170.28080.1640.4734-0.07880.04870.0046-0.10420.0841-0.0059-0.04220.0347-00.2234-0.04180.0060.2491-0.00320.247819.917233.2899-12.0688
200.1602-0.1568-0.01070.33690.41030.6071-0.0281-0.03250.0093-0.0141-0.03540.0120.0309-0.0706-00.1457-0.01990.01340.1959-0.01810.21447.455426.39593.111
210.09880.1071-0.01780.1283-0.05350.1954-0.17260.51120.0077-0.3190.1636-0.11650.0132-0.16360.01320.6146-0.07970.10440.6271-0.09780.32222.05176.5155-43.8449
220.309-0.3315-0.13680.34350.21310.5821-0.16640.15780.0291-0.11440.1277-0.00580.2081-0.2072-0.02310.3465-0.10370.10530.258-0.1220.176916.3215-4.7633-26.4163
230.10.08510.1060.04590.04860.0452-0.0065-0.0470.30240.23120.1104-0.09520.17470.23700.6911-0.0304-0.00570.4943-0.0960.424927.640493.240382.2078
240.0752-0.0991-0.2326-0.61461.2079-0.4294-0.1246-0.06570.0672-0.43850.1428-0.11740.43280.2557-0.07230.22460.05450.16420.4236-0.19580.394942.6727.78793.9288
250.20240.0996-0.24110.0209-0.05340.1019-0.17420.0491-0.0827-0.0419-0.0564-0.14990.4302-0.0075-0.00380.5582-0.0340.09170.2975-0.05840.37727.495357.220774.2757
260.0743-0.07510.0770.09310.08210.0882-0.0572-0.3337-0.13540.3793-0.077-0.02730.220.5755-00.75220.26380.0080.97740.20040.543516.331857.8795107.1871
270.19120.05780.0690.02460.0050.1763-0.52740.2041-0.34010.02160.0986-0.17790.5414-0.2378-0.07660.88030.13720.31780.25620.13870.5984-1.851448.494399.6798
280.26050.0106-0.12080.08470.00150.1402-0.29510.0187-0.08650.09580.20190.02630.14340.0385-0.00010.47180.03030.09020.27950.03030.32-1.462361.971388.1041
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 72 )A1 - 72
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 102 )A73 - 102
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 199 )A103 - 199
4X-RAY DIFFRACTION4chain 'A' and (resid 200 through 223 )A200 - 223
5X-RAY DIFFRACTION5chain 'A' and (resid 224 through 306 )A224 - 306
6X-RAY DIFFRACTION6chain 'A' and (resid 307 through 338 )A307 - 338
7X-RAY DIFFRACTION7chain 'A' and (resid 339 through 414 )A339 - 414
8X-RAY DIFFRACTION8chain 'A' and (resid 415 through 440 )A415 - 440
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 27 )B2 - 27
10X-RAY DIFFRACTION10chain 'B' and (resid 28 through 88 )B28 - 88
11X-RAY DIFFRACTION11chain 'B' and (resid 89 through 127 )B89 - 127
12X-RAY DIFFRACTION12chain 'B' and (resid 128 through 182 )B128 - 182
13X-RAY DIFFRACTION13chain 'B' and (resid 183 through 215 )B183 - 215
14X-RAY DIFFRACTION14chain 'B' and (resid 216 through 259 )B216 - 259
15X-RAY DIFFRACTION15chain 'B' and (resid 260 through 295 )B260 - 295
16X-RAY DIFFRACTION16chain 'B' and (resid 296 through 372 )B296 - 372
17X-RAY DIFFRACTION17chain 'B' and (resid 373 through 401 )B373 - 401
18X-RAY DIFFRACTION18chain 'B' and (resid 402 through 438 )B402 - 438
19X-RAY DIFFRACTION19chain 'C' and (resid 1 through 197 )C1 - 197
20X-RAY DIFFRACTION20chain 'C' and (resid 198 through 440 )C198 - 440
21X-RAY DIFFRACTION21chain 'D' and (resid 2 through 127 )D2 - 127
22X-RAY DIFFRACTION22chain 'D' and (resid 128 through 441 )D128 - 441
23X-RAY DIFFRACTION23chain 'E' and (resid 6 through 46 )E6 - 46
24X-RAY DIFFRACTION24chain 'E' and (resid 47 through 144 )E47 - 144
25X-RAY DIFFRACTION25chain 'F' and (resid 1 through 83 )F1 - 83
26X-RAY DIFFRACTION26chain 'F' and (resid 84 through 198 )F84 - 198
27X-RAY DIFFRACTION27chain 'F' and (resid 199 through 283 )F199 - 283
28X-RAY DIFFRACTION28chain 'F' and (resid 284 through 384 )F284 - 384

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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