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- PDB-5s4p: Tubulin-Z275165822-complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5s4p
TitleTubulin-Z275165822-complex
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin-Tyrosine Ligase
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 / cytoplasmic microtubule / microtubule-based process / 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 / cytoplasmic microtubule / microtubule-based process / tubulin binding / cellular response to interleukin-4 / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / mitotic cell cycle / double-stranded RNA binding / 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 / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Rossmann fold - #11480 / 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. ...Rossmann fold - #11480 / 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. / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / 1-[4-(4-chlorophenyl)piperazin-1-yl]ethan-1-one / 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: 2.29 Å
AuthorsMuehlethaler, T. / Gioia, D. / Prota, A.E. / Sharpe, M.E. / Cavalli, A. / Steinmetz, M.O.
Funding supportEuropean Union, Italy, Switzerland, 4items
OrganizationGrant numberCountry
iNEXT/Horizon 2020PID2692European Union
NEON/Regione LombardiaID239047 Italy
Swiss National Science Foundation31003A_166608 Switzerland
Swiss National Science Foundation31030A_192566 Switzerland
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Comprehensive Analysis of Binding Sites in Tubulin.
Authors: Muhlethaler, T. / Gioia, D. / Prota, A.E. / Sharpe, M.E. / Cavalli, A. / Steinmetz, M.O.
History
DepositionNov 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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-2B chain
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Stathmin-4
F: Tubulin-Tyrosine Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,74026
Polymers261,6316
Non-polymers4,10920
Water6,720373
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.246, 157.049, 178.157
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: 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
#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
#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
#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 , 8 types, 393 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-WNY / 1-[4-(4-chlorophenyl)piperazin-1-yl]ethan-1-one


Mass: 238.713 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H15ClN2O / Feature type: SUBJECT OF INVESTIGATION
#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.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#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.: 373 / 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, 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
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.29→78.52 Å / Num. obs: 133558 / % possible obs: 100 % / Redundancy: 6.758 % / Biso Wilson estimate: 68.137 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.142 / Χ2: 0.837 / Net I/σ(I): 7.3 / Num. measured all: 902641 / Scaling rejects: 163
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
2.29-2.356.5971.7481.0464514978297800.5041.898100
2.35-2.416.9991.3591.3966656952695230.6171.469100
2.41-2.487.071.0391.8365826931193100.7311.121100
2.48-2.567.0020.8342.2463136901790170.8230.901100
2.56-2.646.8910.6322.8660075871987180.8730.684100
2.64-2.746.740.513.4757081847084690.8980.553100
2.74-2.846.4990.3844.2853378821582130.9430.418100
2.84-2.966.7240.3015.452712784078390.9570.326100
2.96-3.096.9990.2286.9953017757575750.9740.247100
3.09-3.246.9190.1848.3950069723772360.980.199100
3.24-3.416.8390.1510.0547071688568830.9840.162100
3.41-3.626.4680.13111.2442364655365500.9820.143100
3.62-3.876.4550.11612.8839722615461540.9860.127100
3.87-4.186.9610.10914.5739990574557450.9860.118100
4.18-4.586.8380.10115.7636140528752850.9890.11100
4.58-5.126.5670.115.8831700482848270.9870.108100
5.12-5.916.1810.10215.3326364426842650.9840.11199.9
5.91-7.246.7960.10316.5124778364636460.9820.112100
7.24-10.246.2370.09916.917838286228600.9870.10999.9
10.24-78.526.140.117.4510210167316630.9850.1199.4

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Processing

Software
NameVersionClassificationNB
PHENIX1.18.2_3874refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5lxt

5lxt


Resolution: 2.29→78.52 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 1962 1.52 %
Rwork0.2077 126980 -
obs0.2083 128942 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.96 Å2 / Biso mean: 63.7441 Å2 / Biso min: 25.64 Å2
Refinement stepCycle: final / Resolution: 2.29→78.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17396 0 327 373 18096
Biso mean--60.09 51.64 -
Num. residues----2198
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.29-2.350.41991360.37538616875294
2.35-2.410.37571370.34458731886895
2.41-2.480.38381340.31598789892396
2.48-2.560.30891360.29798844898096
2.56-2.650.32741390.2798910904997
2.65-2.760.31621400.27428942908297
2.76-2.890.28411360.25939015915198
2.89-3.040.32341420.24639103924598
3.04-3.230.29151400.22519160930099
3.23-3.480.21121400.20469250939099
3.48-3.830.21971430.187592299372100
3.83-4.380.21171440.163993139457100
4.38-5.520.18121460.162793939539100
5.52-78.520.20721490.177396859834100
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)
11.8332-0.5675-0.27835.29361.0812.76850.00460.10820.2392-0.35180.1823-0.2569-0.62680.1845-0.19280.4749-0.07020.0960.4015-0.11650.377131.93889.350550.1196
22.45480.0218-2.09075.13090.16282.63020.0242-0.3292-0.04030.5849-0.0983-0.08970.14350.14320.10780.37050.0725-0.03060.3381-0.10830.30830.085973.894258.4279
31.9383-0.21930.07713.43250.47644.43560.14050.00190.0940.4733-0.05140.3666-0.1934-0.2129-0.05060.41490.04510.11210.3573-0.10810.408317.122484.069666.2064
40.99290.056-0.06212.93061.28952.2134-0.0651-0.29360.23430.96470.12570.3246-0.0755-0.0764-0.08190.67980.06750.13450.4862-0.10980.453619.078782.862972.6039
51.23330.95592.03744.83812.59417.6197-0.0288-0.1461-0.18610.65730.2349-0.36590.53840.5155-0.14210.41850.1522-0.05060.3621-0.11630.471632.667561.927360.9603
65.8821-1.4835-0.43167.20310.51843.54860.21920.21920.6947-0.4546-0.14660.3725-0.9059-0.2283-0.02310.51590.06350.01740.3536-0.01070.37415.769969.729818.6847
71.8916-0.2115-0.05282.31151.27183.6346-0.004-0.00450.0291-0.0511-0.03730.0808-0.3004-0.08830.00250.3268-0.00660.03480.3868-0.1070.386920.101955.81324.8329
84.0642-1.5371.2542.9857-0.74033.7136-0.14-0.1125-0.050.26090.00430.5167-0.2456-1.20960.11030.49140.05220.10720.7133-0.17690.51846.117159.744742.3318
90.9787-0.9543-0.6374.45042.49084.6473-0.041-0.2262-0.09580.74970.07260.17820.72810.1548-0.05510.3172-0.04860.01420.4105-0.04320.402821.200541.053730.9
101.7399-0.64810.00323.06240.01781.9326-0.00070.22760.101-0.22280.0818-0.0409-0.25530.1278-0.07610.3441-0.08370.03690.3799-0.04560.31120.386632.5091-12.0069
111.6845-0.93780.07582.10740.94241.8942-0.0231-0.05130.0540.0912-0.03720.09360.0108-0.23430.05730.2439-0.07130.04110.293-0.02810.30058.233825.47083.159
124.8831-1.8348-0.45596.03320.23632.5806-0.11240.89910.23-0.63880.27370.10610.0097-0.2448-0.1540.5191-0.17640.05680.81610.00260.346617.34479.0359-44.0224
131.77120.0336-0.35251.5961-0.03572.4715-0.0860.4627-0.2361-0.31690.206-0.3280.2590.1962-0.10670.531-0.0670.10170.6534-0.24170.474122.9306-2.8643-34.085
143.6245-1.9241.34964.780.22420.9375-0.01340.2438-0.5947-0.3144-0.13780.74060.3539-0.63770.08860.5544-0.15890.01950.7809-0.21590.5532.0689-6.797-24.9931
152.5398-0.55730.19212.1479-0.55712.7505-0.1530.2646-0.28690.06180.18330.25210.2154-0.41930.0040.5043-0.1180.04950.4521-0.13580.43528.9137-2.1916-20.7395
162.6966-0.0076-0.74943.98110.24972.6222-0.29790.1972-0.7545-0.01460.0158-0.23540.60880.39780.11210.7030.08330.03870.59-0.27150.788930.4999-17.708-24.2733
174.5094-3.91-2.08795.15862.02212.9603-0.3794-0.69480.22591.45370.6741-0.5062-0.15930.819-0.31211.3602-0.1267-0.09560.8021-0.27090.717127.749792.638481.0261
180.2054-0.2268-0.40080.56020.53640.7257-0.15760.077-0.06530.47670.6726-0.4650.6331.0262-0.57540.49050.10910.03030.7322-0.26370.726743.117427.76413.8111
192.75351.4084-0.99356.69171.17442.292-0.55240.6535-0.6776-0.29760.3632-0.061.5837-0.58350.11641.0569-0.21930.17870.648-0.140.59096.7754.107968.9392
207.72141.51654.62715.5444-2.81999.03140.0517-0.850.12290.2921-0.2523-0.7077-0.10261.37390.17260.62910.11620.04970.8305-0.02720.594115.547264.108101.9243
213.84980.6662.79724.0801-0.95144.33650.1378-0.1146-0.68850.4123-0.045-0.86721.12391.2493-0.00340.93930.34190.02550.76230.08350.789111.907151.4833104.5611
222.67010.7845-0.66393.0804-1.00371.701-0.29260.0953-0.7870.21960.2698-0.23661.0296-0.084-0.06671.11530.08470.16870.47160.04980.7502-1.971649.148398.4908
233.25590.2205-2.29470.09330.21163.8941-0.33280.1988-0.37530.06490.42510.01710.8617-0.2949-0.13860.81540.00440.09630.36940.03650.52081.246757.490586.7648
244.675-3.1528-2.38332.32420.63855.97990.12520.65350.2473-0.04930.32920.46820.0079-1.1683-0.3910.4461-0.16530.00540.79980.12810.6907-7.967262.218978.4198
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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