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- PDB-8a9t: Tubulin-[1,2]oxazoloisoindole-1 complex -

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Basic information

Entry
Database: PDB / ID: 8a9t
TitleTubulin-[1,2]oxazoloisoindole-1 complex
Components
  • (Tubulin beta-2B ...) x 2
  • Stathmin-4
  • Tubulin alpha-1B chain
KeywordsCELL CYCLE / TUBULIN FOLD / CYTOSKELETON / MICROTUBULE
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / spindle microtubule / structural constituent of cytoskeleton ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / nervous system development / mitotic cell cycle / growth cone / microtubule / neuron projection / protein heterodimerization activity / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytosol / 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. / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / 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 / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / IMIDAZOLE / Chem-LNU / Tubulin tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Gallus gallus (chicken)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.304 Å
AuthorsProta, A.E. / Abel, A.-C. / Steinmetz, M.O. / Barraja, P. / Montalbano, A. / Spano, V.
Funding support Italy, United States, European Union, Switzerland, 4items
OrganizationGrant numberCountry
Ministero dell Universita e della RicercaMIUR Italy
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001E United States
European Commission860070 TubInTrainEuropean Union
Swiss National Science Foundation31003A_166608 Switzerland
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Development of [1,2]oxazoloisoindoles tubulin polymerization inhibitors: Further chemical modifications and potential therapeutic effects against lymphomas.
Authors: Barreca, M. / Spano, V. / Rocca, R. / Bivacqua, R. / Abel, A.C. / Maruca, A. / Montalbano, A. / Raimondi, M.V. / Tarantelli, C. / Gaudio, E. / Cascione, L. / Rinaldi, A. / Bai, R. / ...Authors: Barreca, M. / Spano, V. / Rocca, R. / Bivacqua, R. / Abel, A.C. / Maruca, A. / Montalbano, A. / Raimondi, M.V. / Tarantelli, C. / Gaudio, E. / Cascione, L. / Rinaldi, A. / Bai, R. / Steinmetz, M.O. / Prota, A.E. / Alcaro, S. / Hamel, E. / Bertoni, F. / Barraja, P.
History
DepositionJun 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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-2B chain
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Stathmin-4
F: Tubulin beta-2B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,02823
Polymers261,6316
Non-polymers3,39617
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.212, 158.054, 180.717
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 , 2 types, 3 molecules ACE

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


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Brain / References: UniProt: P81947
#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.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043

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Tubulin beta-2B ... , 2 types, 3 molecules BDF

#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Brain / References: UniProt: Q6B856
#4: Protein Tubulin beta-2B chain


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, 329 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine 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.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


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


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-LNU / ethyl 13-[(3,5-dimethoxyphenyl)methyl]-3-oxa-4,13-diazatricyclo[8.3.0.0^{2,6}]trideca-1(10),2(6),4,11-tetraene-12-carboxylate


Mass: 396.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24N2O5 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#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 / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.8 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 4% PEG 4K, 8% glycerol, 30 mM MgCl2, 30 mM CaCl2, 0.1 M MES/Imidazole, 5 mM L-tyrosine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999999 Å / Relative weight: 1
ReflectionResolution: 2.3→49.632 Å / Num. obs: 257119 / % possible obs: 99.9 % / Redundancy: 6.994 % / Biso Wilson estimate: 53.43 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.188 / Rrim(I) all: 0.203 / Χ2: 0.755 / Net I/σ(I): 9.34 / Num. measured all: 1798313
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.446.5663.2450.5327242141605414890.1393.52399.7
2.44-2.617.0312.060.9227470439081390690.3382.223100
2.61-2.826.8021.2741.4924729336358363540.5661.379100
2.82-3.097.2730.677324312333433334280.8410.728100
3.09-3.457.3310.3286.2622175530249302470.960.353100
3.45-3.987.1260.14314.0719036826714267140.9920.154100
3.98-4.876.760.06526.5915277322601226010.9980.071100
4.87-6.857.050.05929.9312306317455174550.9980.063100
6.85-49.6327.4590.03251.3872813979197620.9990.03599.7

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata scaling
PDB_EXTRACT3.28data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LXT

5lxt


Resolution: 2.304→47.91 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2366 --
Rwork0.1942 --
obs0.1963 133286 99.93 %
Refinement stepCycle: final / Resolution: 2.304→47.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17083 0 211 312 17606
Biso mean--75.25 63.02 -
Num. residues----2159
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.304-2.330.41744190.4018803298
2.33-2.360.36624310.35428097100
2.36-2.390.37184350.34998185100
2.39-2.420.3644270.33628088100
2.42-2.450.33634260.33298206100
2.45-2.480.37494270.32718070100
2.48-2.520.33264340.32678195100
2.52-2.560.36734310.32618176100
2.56-2.590.35334230.31158145100
2.6-2.640.35174300.30978154100
2.64-2.680.36184240.29158103100
2.68-2.730.32574280.27828124100
2.73-2.780.32044310.2718164100
2.78-2.840.29264250.25978160100
2.84-2.90.31284260.24858125100
2.9-2.970.27014260.24128125100
2.97-3.040.29214360.23968157100
3.04-3.130.2624340.21328173100
3.13-3.220.24894280.20568153100
3.22-3.320.22564300.19688120100
3.32-3.440.23734240.19218145100
3.44-3.580.21854350.17818132100
3.58-3.740.254290.16588182100
3.74-3.940.1974340.15388125100
3.94-4.190.19174260.14738153100
4.19-4.510.17854280.13328145100
4.51-4.960.16964250.12348148100
4.96-5.680.19134280.15618134100
5.68-7.150.24374290.18058140100
7.15-47.910.18024280.16068133100
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)
11.1883-0.6974-0.6082.0617-0.12341.2628-0.04010.18630.3138-0.60460.28130.032-0.93240.1885-0.00010.9087-0.1190.10540.5912-0.15030.615128.457596.304952.3903
20.73690.15390.92110.21440.28951.17-0.0780.2672-0.1052-0.7150.03830.1436-0.8652-0.0327-0.00020.9981-0.06280.13110.6456-0.09090.668329.415987.234743.38
30.260.1869-0.22064.15160.93882.8528-0.04690.0061-0.0394-0.00740.3076-0.6307-0.17060.599300.4755-0.03040.03150.6357-0.2340.630735.252278.477655.204
40.4379-0.2413-0.58391.29560.0060.91360.2691-0.1962-0.60710.16430.07350.527-0.0135-0.50090.00020.60430.04520.03580.6034-0.12030.774411.793379.290160.0746
50.71450.0744-0.81571.02070.31841.0734-0.07530.18070.07270.19490.1751-0.0129-0.54450.48540.00010.7025-0.01530.04260.5981-0.12870.654825.164290.588865.4629
61.57921.5724-0.43872.58840.87743.14660.3105-0.2290.23430.3752-0.19970.5621-0.0786-0.3579-0.00020.6451-0.01060.11980.5431-0.15920.630814.102384.301471.0876
70.86070.30370.59110.33450.41770.57970.1747-0.39340.15560.95-0.07830.4856-0.2222-0.13170.00030.9109-0.02410.17640.553-0.13070.595717.526587.855480.199
80.4862-0.0377-0.24453.11541.54922.4560.0297-0.146-0.01790.63460.15330.03390.18750.31460.00020.59280.03060.02250.5411-0.13150.573424.676473.53767.4936
92.1028-0.986-0.31951.7898-0.62741.964-0.00730.17790.463-0.4096-0.02410.1495-0.8883-0.2894-00.72230.0885-0.0360.5232-0.03290.678616.234470.094119.4468
101.5881-0.5377-0.50092.15561.42953.4138-0.01550.0760.1493-0.1129-0.01660.012-0.1763-0.0188-0.00460.3860.03290.00290.484-0.09680.490920.508454.107123.5137
110.6075-0.3819-0.18681.5856-0.28223.0150.1552-0.10810.2913-0.1754-0.0980.1991-0.2474-0.498300.5070.0699-0.00680.5387-0.21940.61879.967862.579737.9891
120.5435-0.18860.36151.87341.29942.8821-0.0875-0.19460.0240.5308-0.15630.2680.1991-0.3975-0.00290.4721-0.02140.060.5828-0.08950.566513.864850.375238.6763
132.0845-0.7932-0.18751.448-0.51391.5234-0.0310.22180.3944-0.2338-0.08070.1845-0.4636-0.06090.00010.554-0.04050.0040.5318-0.00350.528714.408242.8144-13.073
141.3169-0.66950.18062.65220.73362.5027-0.05910.2595-0.0162-0.45920.1799-0.2003-0.24710.2454-0.00010.4253-0.11010.07150.5187-0.0440.475424.807630.8293-14.4691
150.8221-0.8883-0.2451.9195-0.64751.7092-0.08440.0433-0.02920.0008-0.00560.2640.16350.173500.42130.00620.00380.4833-0.07710.471420.228220.8322-3.8232
161.4115-0.66360.42871.28560.97233.15960.02740.00790.0780.0566-0.20880.24740.0646-0.4415-0.00080.3774-0.05320.03740.4531-0.06020.54042.712630.15332.6141
171.4202-0.07070.36991.19280.90831.0549-0.0172-0.16110.0469-0.16080.06670.3640.0006-0.4246-0.00010.447-0.04930.02180.4821-0.07840.57012.225334.38686.1069
180.3133-0.2984-0.07161.33161.01221.5919-0.05990.0634-0.0550.33170.127-0.17510.3880.148100.4305-0.00350.00340.3771-0.06260.492320.136113.48492.5537
192.2044-0.48240.56650.562-0.02611.2121-0.17460.60490.3985-0.36520.26140.0695-0.108-0.3693-00.7628-0.11280.01011.0417-0.02320.593915.49612.4469-41.8523
202.43980.0489-0.34631.80090.12522.5885-0.14470.6877-0.2722-0.53190.2152-0.31860.31530.1989-0.0020.7913-0.08730.10640.8667-0.27490.586825.2783-3.1975-38.9603
211.0472-0.10490.01530.9752-0.5270.6963-0.18270.3770.2555-0.35750.22060.4454-0.2446-0.3214-0.00010.6092-0.06180.04080.7792-0.07710.587813.50535.2345-30.4087
221.4921-0.025-0.48221.80420.64782.4657-0.19120.3974-0.3124-0.07410.1745-0.01740.4462-0.26470.00120.6994-0.12330.04980.6312-0.16890.61413.9004-6.7116-23.0828
230.5598-0.20960.05950.4668-0.03090.26920.0079-0.05810.59240.2416-0.1179-0.7994-0.45870.8668-0.00611.1612-0.14920.0620.79-0.26330.889324.916399.637781.9955
240.1158-0.04940.01830.11110.03590.0759-0.423-0.2505-0.80230.80050.0955-0.6240.28550.7340.00081.6510.0357-0.04131.0163-0.15991.00432.032382.914282.2462
250.4991-0.3107-0.56530.18830.25220.8304-0.020.0084-0.05410.27050.4096-0.43610.42910.55070.00650.55360.060.01350.8351-0.24660.774143.135628.30014.4034
261.75390.2548-1.7720.99490.26612.0543-0.31870.3585-0.5605-0.0798-0.0334-0.32510.9449-0.1549-0.00011.0621-0.09290.10720.7399-0.150.79846.220254.95269.7931
270.40990.1623-0.00810.2652-0.21490.2526-0.08-0.63790.18310.66650.0043-0.3634-0.42691.4269-01.040.0190.08861.0893-0.01280.752810.905766.15597.5402
280.06510.06860.01170.08770.04460.0426-0.3081-0.3880.40510.467-0.4306-1.1033-0.07030.58370.00011.06750.0222-0.31722.11510.24761.247321.387562.0787110.6128
290.4115-0.37870.32550.6014-0.02550.6567-0.2801-0.4489-0.45510.5891-0.1553-0.38621.25961.6952-0.00151.33180.3140.02351.7960.48831.300113.094651.7412109.2739
302.9232-0.3217-2.21610.81960.45613.1758-0.3997-0.0461-0.61560.1830.25430.1570.7497-0.1388-0.01591.04050.02410.10850.57510.04230.793-2.756156.634192.9411
310.4791-0.25930.13770.3805-0.2820.3690.05420.8228-0.19010.0850.23120.1153-0.0456-1.29400.8485-0.09420.0480.9197-0.07430.9101-8.698962.739979.6528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 80 )A1 - 80
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 102 )A81 - 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 259 )A224 - 259
6X-RAY DIFFRACTION6chain 'A' and (resid 260 through 306 )A260 - 306
7X-RAY DIFFRACTION7chain 'A' and (resid 307 through 336 )A307 - 336
8X-RAY DIFFRACTION8chain 'A' and (resid 337 through 437 )A337 - 437
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 88 )B1 - 88
10X-RAY DIFFRACTION10chain 'B' and (resid 89 through 238 )B89 - 238
11X-RAY DIFFRACTION11chain 'B' and (resid 239 through 295 )B239 - 295
12X-RAY DIFFRACTION12chain 'B' and (resid 296 through 438 )B296 - 438
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 72 )C1 - 72
14X-RAY DIFFRACTION14chain 'C' and (resid 73 through 161 )C73 - 161
15X-RAY DIFFRACTION15chain 'C' and (resid 162 through 199 )C162 - 199
16X-RAY DIFFRACTION16chain 'C' and (resid 200 through 338 )C200 - 338
17X-RAY DIFFRACTION17chain 'C' and (resid 339 through 372 )C339 - 372
18X-RAY DIFFRACTION18chain 'C' and (resid 373 through 440 )C373 - 440
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 64 )D1 - 64
20X-RAY DIFFRACTION20chain 'D' and (resid 65 through 223 )D65 - 223
21X-RAY DIFFRACTION21chain 'D' and (resid 224 through 259 )D224 - 259
22X-RAY DIFFRACTION22chain 'D' and (resid 260 through 440 )D260 - 440
23X-RAY DIFFRACTION23chain 'E' and (resid 6 through 20 )E6 - 20
24X-RAY DIFFRACTION24chain 'E' and (resid 21 through 46 )E21 - 46
25X-RAY DIFFRACTION25chain 'E' and (resid 47 through 142 )E47 - 142
26X-RAY DIFFRACTION26chain 'F' and (resid 1 through 66 )F1 - 66
27X-RAY DIFFRACTION27chain 'F' and (resid 67 through 96 )F67 - 96
28X-RAY DIFFRACTION28chain 'F' and (resid 97 through 140 )F97 - 140
29X-RAY DIFFRACTION29chain 'F' and (resid 141 through 198 )F141 - 198
30X-RAY DIFFRACTION30chain 'F' and (resid 199 through 354 )F199 - 354
31X-RAY DIFFRACTION31chain 'F' and (resid 355 through 381 )F355 - 381

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