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- PDB-7z2p: Tubulin-nocodazole complex -

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Basic information

Entry
Database: PDB / ID: 7z2p
TitleTubulin-nocodazole 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 / cellular response to interleukin-4 / tubulin binding / 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 / cellular response to interleukin-4 / tubulin binding / 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 / cytosol / cytoplasm
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 / nocodazole / 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 Å
AuthorsProta, A.E. / Muehlethaler, T. / Cavalli, A. / Steinmetz, M.O.
Funding support Switzerland, European Union, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166608 Switzerland
European CommissionID239047 NEONEuropean Union
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Novel fragment-derived colchicine-site binders as microtubule-destabilizing agents.
Authors: de la Roche, N.M. / Muhlethaler, T. / Di Martino, R.M.C. / Ortega, J.A. / Gioia, D. / Roy, B. / Prota, A.E. / Steinmetz, M.O. / Cavalli, A.
History
DepositionFeb 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 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)265,18420
Polymers261,6316
Non-polymers3,55314
Water13,998777
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)104.732, 158.090, 179.553
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 , 7 types, 791 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.: 5 / Source method: obtained synthetically / Formula: Mg
#7: 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
#8: 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
#9: Chemical ChemComp-NW6 / nocodazole


Mass: 301.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11N3O3S / Feature type: SUBJECT OF INVESTIGATION
#10: 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
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 777 / 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: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2% PEG 4K, 4% 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: X10SA / Wavelength: 0.97976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97976 Å / Relative weight: 1
ReflectionResolution: 2→49.37 Å / Num. obs: 200305 / % possible obs: 99.77 % / Redundancy: 13.5 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1231 / Rpim(I) all: 0.03467 / Rrim(I) all: 0.128 / Net I/σ(I): 14.63
Reflection shellResolution: 2→2.072 Å / Num. unique obs: 19421 / CC1/2: 0.393

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LXT

5lxt


Resolution: 2→49.37 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 21.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 19421 4.99 %
Rwork0.1784 368517 -
obs0.1799 200301 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.98 Å2 / Biso mean: 50.451 Å2 / Biso min: 18.39 Å2
Refinement stepCycle: final / Resolution: 2→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17335 0 244 777 18356
Biso mean--41.58 47.43 -
Num. residues----2190
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.020.37645880.3479111571174590
2.02-2.050.32446490.30731228812937100
2.05-2.070.34356470.30231228812935100
2.07-2.10.32456480.29231235213000100
2.1-2.130.30866470.27671236113008100
2.13-2.150.28646450.26821230312948100
2.15-2.190.28026470.2541236313010100
2.19-2.220.26146480.24381227612924100
2.22-2.250.25566410.22931233512976100
2.25-2.290.23626480.22131231912967100
2.29-2.330.24566510.22321231912970100
2.33-2.370.24746470.21591233612983100
2.37-2.420.24286460.20391231712963100
2.42-2.470.22726490.19091233412983100
2.47-2.520.22366450.18871229112936100
2.52-2.580.22466500.18411232312973100
2.58-2.640.23116410.18491233312974100
2.64-2.710.23456490.18681234012989100
2.71-2.790.21996510.19111229212943100
2.79-2.880.23066500.19341236313013100
2.88-2.990.23056500.18481233012980100
2.99-3.110.20576470.17371234712994100
3.11-3.250.23316460.18321230412950100
3.25-3.420.21666480.17921231612964100
3.42-3.630.19456580.16121232812986100
3.63-3.910.17846410.14781233012971100
3.91-4.310.16636520.13671229612948100
4.31-4.930.14566500.12541232412974100
4.93-6.210.18276500.16051231512965100
6.21-49.370.17136440.15441233712981100
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)
10.72630.1216-0.14552.51570.78152.041-0.0310.07770.0739-0.20030.216-0.2406-0.45530.3333-0.16320.3771-0.08610.06680.3632-0.13150.338931.699986.634852.2879
21.2722-0.1566-0.03082.03130.2152.24520.11760.0534-0.06610.23270.00410.0237-0.10010.0767-0.09810.33460.01610.05580.2902-0.09510.351121.078984.57964.4692
30.86180.6708-0.41181.15970.61272.55160.27570.08330.02560.0923-0.27050.59250.0819-0.47-0.0160.415-0.00760.14450.3963-0.14550.49559.344484.601671.2622
40.36520.13080.07482.60861.27251.97250.0102-0.0958-0.0160.57470.02990.12420.17650.0552-0.03440.3723-0.00310.05480.321-0.0840.312923.18277.009869.8342
51.8535-0.3252-0.15951.7991-0.10771.53860.03720.03480.3996-0.2015-0.06060.2028-0.6439-0.1602-0.01270.43540.0421-0.00010.3006-0.06390.421914.912971.94322.6013
61.9784-1.17280.17013.35840.68991.97110.21390.33970.1026-1.0906-0.26520.1356-0.7035-0.10280.09310.48790.0408-0.02550.3166-0.02190.35717.929266.841612.7992
71.2917-0.4232-0.15671.58680.72381.75040.0430.04570.1327-0.16780.0682-0.1328-0.26250.178-0.10410.2521-0.01680.0360.351-0.10150.32426.544556.385520.7871
80.1606-0.4604-0.22451.43420.62691.942-0.0698-0.1026-0.0330.1275-0.13460.31040.0662-0.35480.15520.2291-0.01850.0260.3568-0.13210.389911.331950.775527.1937
91.29850.1570.72550.3048-0.36332.17380.02050.0310.18550.2362-0.09430.0334-0.37760.00740.0570.32280.00450.05020.3162-0.12850.383620.22964.116539.1352
101.167-0.5479-0.14461.92540.86271.0288-0.1113-0.0441-0.1180.1234-0.19030.34180.0417-0.57550.28010.3402-0.05310.06910.5413-0.18520.49131.648756.457738.8623
112.3388-1.1367-0.47740.9520.39961.3744-0.3679-0.21980.1930.63680.15910.1674-0.441-0.7430.16830.44970.1070.0570.5603-0.15440.46664.448264.88846.871
121.9167-0.28110.45230.88160.32881.6665-0.1383-0.17670.14640.22610.01570.1941-0.0237-0.59570.1080.32650.02290.04760.3894-0.15990.41469.030662.477844.9002
130.5338-0.3847-0.05330.92851.04691.7821-0.0477-0.0957-0.03690.4553-0.17570.53020.4198-0.2290.16960.3159-0.02830.06960.3342-0.08040.329815.024143.224834.2933
140.63330.16910.33062.05971.08432.22350.0126-0.0446-0.12640.4941-0.0411-0.16060.56960.1524-0.01440.30610.0245-0.06150.299-0.02880.295726.030138.104530.9573
150.946-0.2984-0.01662.09970.32931.3986-0.04460.12410.0906-0.20140.106-0.0595-0.12680.1655-0.04450.2276-0.060.03810.2931-0.02430.263820.468232.9557-11.8308
160.8119-0.46310.05071.29440.88891.2445-0.0179-0.01850.02830.0884-0.05660.08710.1027-0.15030.06740.2158-0.05220.04050.2623-0.02060.26867.886925.97723.2019
173.11750.2682-0.21892.1578-0.59721.87110.00830.57910.2461-0.33840.14420.21290.0526-0.043-0.15880.4289-0.08560.05680.5906-0.03560.282117.35679.7244-44.1584
181.8865-0.2683-0.57611.2637-0.19081.9362-0.04330.316-0.1836-0.21510.121-0.22090.19850.1751-0.04660.4388-0.02010.06980.4883-0.19190.340924.3704-4.0619-36.8363
191.4097-0.06480.25060.69670.58881.20050.00760.2407-0.0356-0.287-0.0030.04280.1052-0.1124-0.02490.3157-0.04330.02760.3971-0.09080.307811.94543.7531-24.051
201.5315-0.4138-0.35741.2434-0.03281.738-0.17930.229-0.2520.00650.09110.21490.2299-0.19470.08090.3976-0.07030.0230.3576-0.09910.3258.5618-3.1124-21.0528
211.9901-0.3585-1.18791.06530.71271.9267-0.3856-0.0809-0.82480.15150.0644-0.070.60130.61-0.06560.62540.09780.05740.4928-0.19530.615430.4937-17.1939-24.5197
221.5804-0.2607-0.16880.32940.09710.9715-0.2191-0.21910.16790.69110.3302-0.36120.19050.4985-0.12520.8445-0.03530.02260.4678-0.16830.479927.621893.025281.6872
230.129-0.2319-0.30810.15570.09680.3423-0.0967-0.0102-0.02730.01470.545-0.41830.09840.762-0.33890.30750.0430.02560.6145-0.24860.522343.177827.90123.8636
241.22850.7641-0.40283.1985-0.03110.612-0.59770.5757-0.5474-0.30180.079-0.27191.502-0.3180.14910.9674-0.19360.21990.4942-0.17820.46676.60754.662169.6962
251.36730.42090.76621.199-0.8062.18860.0165-0.8785-0.2940.2643-0.3541-0.77650.10941.56760.24480.64330.1746-0.05241.25040.22650.669317.786659.8168104.474
262.32920.6439-1.99880.96070.05192.0983-0.4966-0.065-0.63240.15210.1787-0.07710.8928-0.0380.00560.79910.03080.14330.32090.06180.5485-1.303553.141894.7625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 199 )A1 - 199
2X-RAY DIFFRACTION2chain 'A' and (resid 200 through 273 )A200 - 273
3X-RAY DIFFRACTION3chain 'A' and (resid 274 through 311 )A274 - 311
4X-RAY DIFFRACTION4chain 'A' and (resid 312 through 439 )A312 - 439
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 56 )B1 - 56
6X-RAY DIFFRACTION6chain 'B' and (resid 57 through 88 )B57 - 88
7X-RAY DIFFRACTION7chain 'B' and (resid 89 through 180 )B89 - 180
8X-RAY DIFFRACTION8chain 'B' and (resid 181 through 238 )B181 - 238
9X-RAY DIFFRACTION9chain 'B' and (resid 239 through 268 )B239 - 268
10X-RAY DIFFRACTION10chain 'B' and (resid 269 through 311 )B269 - 311
11X-RAY DIFFRACTION11chain 'B' and (resid 312 through 338 )B312 - 338
12X-RAY DIFFRACTION12chain 'B' and (resid 339 through 372 )B339 - 372
13X-RAY DIFFRACTION13chain 'B' and (resid 373 through 401 )B373 - 401
14X-RAY DIFFRACTION14chain 'B' and (resid 402 through 438 )B402 - 438
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 199 )C1 - 199
16X-RAY DIFFRACTION16chain 'C' and (resid 200 through 440 )C200 - 440
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 88 )D1 - 88
18X-RAY DIFFRACTION18chain 'D' and (resid 89 through 238 )D89 - 238
19X-RAY DIFFRACTION19chain 'D' and (resid 239 through 295 )D239 - 295
20X-RAY DIFFRACTION20chain 'D' and (resid 296 through 399 )D296 - 399
21X-RAY DIFFRACTION21chain 'D' and (resid 400 through 441 )D400 - 441
22X-RAY DIFFRACTION22chain 'E' and (resid 6 through 46 )E6 - 46
23X-RAY DIFFRACTION23chain 'E' and (resid 47 through 143 )E47 - 143
24X-RAY DIFFRACTION24chain 'F' and (resid 1 through 66 )F1 - 66
25X-RAY DIFFRACTION25chain 'F' and (resid 67 through 184 )F67 - 184
26X-RAY DIFFRACTION26chain 'F' and (resid 185 through 378 )F185 - 378

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