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- PDB-7z2n: Tubulin-18-complex -

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Basic information

Entry
Database: PDB / ID: 7z2n
TitleTubulin-18-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 / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / nervous system development / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / protein heterodimerization activity / GTPase activity / nucleotide binding / 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. / 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 / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-IAZ / 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: 2.17 Å
AuthorsMuehlethaler, T. / Prota, A.E. / 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)264,85222
Polymers261,6316
Non-polymers3,22016
Water11,043613
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)105.016, 157.703, 180.154
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 , 8 types, 629 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / 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-IAZ / ~{N}-(furan-2-ylmethyl)-6-phenoxy-1~{H}-benzimidazol-2-amine


Mass: 305.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H15N3O2 / 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.: 613 / 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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
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: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→49.82 Å / Num. obs: 157766 / % possible obs: 99.9 % / Redundancy: 13.7 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1159 / Rpim(I) all: 0.03234 / Rrim(I) all: 0.1204 / Net I/σ(I): 16.69
Reflection shellResolution: 2.17→2.249 Å / Num. unique obs: 15493 / CC1/2: 0.492 / Rpim(I) all: 0.5793

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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: 2.17→49.82 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 23.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2237 15266 5.01 %
Rwork0.1891 289634 -
obs0.1908 157750 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.46 Å2 / Biso mean: 63.4308 Å2 / Biso min: 29.44 Å2
Refinement stepCycle: final / Resolution: 2.17→49.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17357 0 195 613 18165
Biso mean--54.56 56.75 -
Num. residues----2193
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 (%)
2.17-2.20.33825010.31969430993197
2.2-2.220.32775040.3169958810092100
2.22-2.250.31375050.2975967510180100
2.25-2.280.31315150.2874969110206100
2.28-2.310.32225040.2945961210116100
2.31-2.340.30195050.2881969110196100
2.34-2.370.30675100.2769969210202100
2.37-2.410.29635140.2665961410128100
2.41-2.450.27035090.2488966910178100
2.45-2.490.25795100.2324966110171100
2.49-2.530.25575120.236966810180100
2.53-2.570.27055040.2277971310217100
2.57-2.620.27625110.2264965710168100
2.62-2.680.26115110.2308965010161100
2.68-2.740.25335020.23963510137100
2.74-2.80.2585100.2328966810178100
2.8-2.870.25295180.2251967310191100
2.87-2.950.28515080.2175964710155100
2.95-3.030.22735090.2016971310222100
3.03-3.130.24895020.1964962310125100
3.13-3.240.23335060.2014966210168100
3.24-3.370.22865150.2077970610221100
3.37-3.530.2265070.1884964810155100
3.53-3.710.20465080.1692966510173100
3.71-3.940.20755160.1593970110217100
3.94-4.250.19355120.155963210144100
4.25-4.680.17745120.1386966210174100
4.68-5.350.19815100.1495967810188100
5.35-6.740.21685120.1775965810170100
6.74-49.820.16675040.154965210156100
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)
11.0915-0.3032-0.31112.83140.86182.37880.01090.02790.1052-0.47460.2974-0.2927-0.64980.40390.01310.526-0.14610.11210.461-0.16580.438932.238789.599750.8239
20.3038-0.4327-0.5751.21230.00010.62730.0772-0.1516-0.08640.24330.0593-0.18370.23020.2663-0.00010.43540.0313-0.01340.4938-0.16750.473630.116274.17558.971
31.4137-0.12530.33432.38620.30873.18280.1229-0.0617-0.01060.31350.01840.1919-0.0871-0.04820.00010.43020.01390.07010.3718-0.11790.473617.257884.531466.9105
40.58710.4990.15182.52230.99322.33790.0423-0.14750.0440.56080.02990.2972-0.00960.07810.00010.49390.01890.0750.4539-0.09570.477919.264183.238173.3476
50.80940.9796-0.3161.2867-0.08410.366-0.0805-0.0773-0.26280.54580.281-0.18120.45160.6093-0.00010.52030.1861-0.06460.5012-0.13050.526132.5362.192761.5322
62.0221-0.2745-0.63541.2708-0.53131.05660.2210.38590.4266-0.3655-0.13530.2365-0.5355-0.18210.00010.60420.08840.01490.5355-0.03230.581315.920370.099419.1135
71.6586-0.2033-0.33561.50341.04862.42450.05280.12230.0538-0.097-0.01690-0.2071-0.0102-0.00030.31820.02910.01080.42-0.11280.42120.213156.262325.2403
82.3126-0.2456-0.37622.23370.65582.1966-0.08210.05390.0050.2364-0.14140.2941-0.0161-0.5084-0.00030.34460.01790.04440.5109-0.18240.44156.050759.94342.6769
9-0.01670.08840.60561.48610.75431.70970.0075-0.0501-0.12310.4579-0.00940.02350.50490.13540.00010.42150.0121-0.00180.4418-0.08550.435321.035340.367232.2766
101.3421-0.3130.06721.98750.04771.7878-0.05110.15660.0686-0.23260.1153-0.0444-0.08750.133400.3228-0.07470.03910.3916-0.03840.350820.240433.1549-12.0424
110.8936-0.4412-0.02971.44640.72891.2172-0.0415-0.03660.03940.1101-0.02010.10080.0861-0.1425-00.3195-0.0410.03730.3687-0.04080.39617.763126.03053.1775
122.17870.3590.11331.0964-0.7670.5793-0.08750.69670.3342-0.33340.25240.08250.0967-0.16810.00010.7007-0.10160.05720.8505-0.02430.482417.19519.6422-43.9846
132.00530.3916-0.59861.4436-0.22612.1256-0.11480.4892-0.1508-0.32620.1673-0.22350.14210.1251-0.01260.4845-0.04310.07680.5344-0.20910.374522.7565-2.3264-34.0412
140.2558-0.4822-0.21190.47540.39760.14850.12430.0257-0.5562-0.2022-0.12660.47060.4896-0.6187-0.00030.6522-0.1122-0.02440.8321-0.20350.64672.1973-6.4047-24.5855
150.9076-0.1995-0.50331.49810.05632.219-0.1160.2182-0.2583-0.01160.14250.17980.1758-0.29880.00010.5063-0.06730.00110.5215-0.11850.44418.6402-1.7944-20.7252
161.2685-0.23510.5531.074-0.57610.5051-0.23760.0879-0.75340.15140.01720.11850.65590.4282-0.02820.74610.05390.09310.588-0.23410.717930.4098-17.2129-24.407
170.4320.15060.17160.34740.3050.1674-0.0256-0.11920.34580.15530.2454-0.81010.23610.65210.00070.9202-0.03-0.02430.6573-0.16840.590427.827792.707881.8987
180.0815-0.543-0.8647-0.00190.22570.4875-0.0091-0.0740.00280.46830.4409-0.49470.55070.64310.04840.4520.1058-0.00640.766-0.28610.684243.071928.08924.0869
191.3847-0.0256-1.54770.61330.62941.8854-0.58010.3-0.4676-0.06660.0276-0.26020.9829-0.3117-0.01130.945-0.12970.18390.5546-0.11030.64396.357254.808569.525
200.25580.1870.05090.10090.25320.4669-0.0971-0.43350.248-0.0849-0.3522-0.4824-0.55031.0748-0.00070.65430.0435-0.06331.16020.14880.704216.485663.7284102.7354
210.67360.23420.47761.6580.37350.7372-0.0922-0.4339-0.69580.3096-0.1387-0.34890.98151.0944-0.26230.92090.3160.11761.1370.40770.831511.020451.8211105.657
221.32410.5812-1.58280.60320.0662.1923-0.48860.0434-0.57220.18470.1323-0.11110.75490.0112-0.05680.99920.09780.2160.41240.13130.7549-2.915850.004998.7143
232.17160.1346-1.6231-0.02430.13891.5564-0.3324-0.092-0.3818-0.02750.1724-0.07330.50850.21170.00010.84450.01540.11050.45030.02940.56231.06758.187487.4735
240.26840.03470.00080.010.03690.11540.01230.23990.15290.20870.14690.1865-0.2631-0.7751-0.00020.7152-0.04240.07490.731-0.01310.6075-7.124963.957779.1374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 160 )A1 - 160
2X-RAY DIFFRACTION2chain 'A' and (resid 161 through 199 )A161 - 199
3X-RAY DIFFRACTION3chain 'A' and (resid 200 through 311 )A200 - 311
4X-RAY DIFFRACTION4chain 'A' and (resid 312 through 401 )A312 - 401
5X-RAY DIFFRACTION5chain 'A' and (resid 402 through 438 )A402 - 438
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 88 )B1 - 88
7X-RAY DIFFRACTION7chain 'B' and (resid 89 through 259 )B89 - 259
8X-RAY DIFFRACTION8chain 'B' and (resid 260 through 372 )B260 - 372
9X-RAY DIFFRACTION9chain 'B' and (resid 373 through 438 )B373 - 438
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 197 )C1 - 197
11X-RAY DIFFRACTION11chain 'C' and (resid 198 through 440 )C198 - 440
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 88 )D1 - 88
13X-RAY DIFFRACTION13chain 'D' and (resid 89 through 273 )D89 - 273
14X-RAY DIFFRACTION14chain 'D' and (resid 274 through 311 )D274 - 311
15X-RAY DIFFRACTION15chain 'D' and (resid 312 through 399 )D312 - 399
16X-RAY DIFFRACTION16chain 'D' and (resid 400 through 441 )D400 - 441
17X-RAY DIFFRACTION17chain 'E' and (resid 6 through 46 )E6 - 46
18X-RAY DIFFRACTION18chain 'E' and (resid 47 through 143 )E47 - 143
19X-RAY DIFFRACTION19chain 'F' and (resid 1 through 66 )F1 - 66
20X-RAY DIFFRACTION20chain 'F' and (resid 67 through 140 )F67 - 140
21X-RAY DIFFRACTION21chain 'F' and (resid 141 through 207 )F141 - 207
22X-RAY DIFFRACTION22chain 'F' and (resid 208 through 297 )F208 - 297
23X-RAY DIFFRACTION23chain 'F' and (resid 298 through 354 )F298 - 354
24X-RAY DIFFRACTION24chain 'F' and (resid 355 through 382 )F355 - 382

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