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- PDB-8a9z: Tubulin-[1,2]oxazoloisoindole-2e complex -

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Basic information

Entry
Database: PDB / ID: 8a9z
TitleTubulin-[1,2]oxazoloisoindole-2e 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 / cytoplasmic microtubule / tubulin binding / cellular response to interleukin-4 / spindle microtubule / protein modification process ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / tubulin binding / cellular response to interleukin-4 / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / neuron projection development / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / cilium / protein heterodimerization activity / nucleotide binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Rossmann fold - #11480 / Helix hairpin bin / 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. ...Rossmann fold - #11480 / Helix hairpin bin / 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/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 60s Ribosomal Protein L30; Chain: A; / 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 / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-LO9 / 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 (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.294 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)265,17923
Polymers261,6316
Non-polymers3,54717
Water7,873437
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)104.500, 155.847, 178.855
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 (domestic 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 (domestic 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 , 8 types, 454 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.: 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


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


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-LO9 / 7-[(3,5-dimethoxyphenyl)methyl]pyrrolo[3,4-g][1,2]benzoxazole


Mass: 308.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H16N2O3 / Feature type: SUBJECT OF INVESTIGATION
#11: 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
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.29→49.887 Å / Num. obs: 252262 / % possible obs: 99.9 % / Redundancy: 7.019 % / Biso Wilson estimate: 52.27 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.225 / Rrim(I) all: 0.243 / Χ2: 0.748 / Net I/σ(I): 8.45 / Num. measured all: 1770704
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
2.29-2.437.0373.7040.4928543340865405640.1263.99899.3
2.43-2.66.7852.3140.8125987538310383030.2882.507100
2.6-2.817.0161.4641.3425049035705357020.5241.581100
2.81-3.086.80.7712.5722372832908329030.7980.835100
3.08-3.447.4030.3835.5221951929654296540.9520.412100
3.44-3.977.2330.16912.518960126216262140.990.182100
3.97-4.856.7240.08123.6414919222188221880.9970.087100
4.85-6.837.0350.06826.9112072417161171600.9980.074100
6.83-49.8877.5350.03449.32721429600957410.03699.7

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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: 2.294→49.887 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2396 --
Rwork0.1991 --
obs0.21 130764 99.86 %
Refinement stepCycle: final / Resolution: 2.294→49.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17095 0 218 437 17750
Biso mean--72.85 63.38 -
Num. residues----2160
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.294-2.320.39024080.4024772096
2.32-2.350.38864170.36277985100
2.35-2.380.37044260.35898015100
2.38-2.410.38234160.34987950100
2.41-2.440.34554240.34188010100
2.44-2.470.37854190.32378024100
2.47-2.510.34224250.32787990100
2.51-2.540.3534220.31447988100
2.54-2.580.33494180.31067994100
2.58-2.630.34524120.30447954100
2.63-2.670.32814260.29698081100
2.67-2.720.33464150.29017933100
2.72-2.770.32394200.28238010100
2.77-2.830.3464260.27748020100
2.83-2.890.29154180.25348010100
2.89-2.960.29914220.24487978100
2.96-3.030.29674260.22757977100
3.03-3.110.26754150.21897973100
3.11-3.210.2594220.21648007100
3.21-3.310.27384280.21158008100
3.31-3.430.2574160.19627998100
3.43-3.560.2414220.1748005100
3.56-3.730.21874230.16578019100
3.73-3.920.19834180.1527990100
3.92-4.170.20324230.15018023100
4.17-4.490.16994280.13857959100
4.49-4.940.18224180.13358016100
4.94-5.660.18064210.15947980100
5.66-7.120.22434200.18998001100
7.12-49.8870.17744270.16217987100
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)
10.98810.1028-0.0592.74411.06112.49270.0604-0.01240.08460.11650.1027-0.0306-0.30810.1514-0.00010.502-0.01080.04220.4957-0.10310.527825.278781.833760.9711
21.0062-0.3511-0.23821.97821.13542.34620.03220.02520.0867-0.0366-0.07150.1115-0.169-0.1322-0.00440.37130.0045-0.00030.4919-0.0840.519816.512556.233729.5815
30.9925-0.06490.12551.21170.50281.6189-0.03550.09570.0934-0.06170.01240.0381-0.103-0.018600.3794-0.04480.01880.4341-0.03690.478513.701528.5138-3.7668
41.60420.1157-0.25021.97720.27662.1153-0.14620.4914-0.1234-0.45730.1683-0.0460.2005-0.0127-00.7002-0.08940.03130.7011-0.16460.523318.3957-1.4294-32.2968
50.19720.0522-0.07920.06650.03110.6786-0.0751-0.03660.0120.18030.4697-0.42360.21320.66340.00030.58380.04110.00010.8379-0.2070.78340.193540.181219.5412
61.97870.4816-1.95241.3511-0.61553.0761-0.137-0.2183-0.49790.22010.0193-0.18550.41380.37960.00010.85870.07050.02410.6130.04490.80984.325655.798291.1746
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 1:503)A1 - 503
2X-RAY DIFFRACTION2(chain B and resseq 1:505)B1 - 505
3X-RAY DIFFRACTION3(chain C and resseq 1:503)C1 - 503
4X-RAY DIFFRACTION4(chain D and resseq 1:503)D1 - 503
5X-RAY DIFFRACTION5(chain E and resseq 6:142)E6 - 142
6X-RAY DIFFRACTION6(chain F and resseq 1:401)F1 - 401

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