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- PDB-8clg: Epothilone A and Colchicine bound to tubulin (T2R-TTL) complex -

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Basic information

Entry
Database: PDB / ID: 8clg
TitleEpothilone A and Colchicine bound to tubulin (T2R-TTL) complex
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin-Tyrosine Ligase
KeywordsCELL CYCLE / Drug-tubulin-complex Cell cycle inhibition
Function / homology
Function and homology information


positive regulation of axon guidance / microtubule-based process / cytoplasmic microtubule / cellular response to interleukin-4 / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton ...positive regulation of axon guidance / microtubule-based process / cytoplasmic microtubule / cellular response to interleukin-4 / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cilium / protein heterodimerization activity / GTPase activity / ubiquitin protein ligase binding / GTP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
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-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 / EPOTHILONE A / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-LOC / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciessynthetic construct (others)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWranik, M. / Bertrand, Q. / Kepa, M.W. / Weinert, T. / Steinmetz, M. / Standfuss, J.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_179351 Switzerland
Swiss National Science Foundation310030_207462 Switzerland
Swiss National Science Foundation310030_192566 Switzerland
CitationJournal: Nat Commun / Year: 2023
Title: A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers.
Authors: Wranik, M. / Kepa, M.W. / Beale, E.V. / James, D. / Bertrand, Q. / Weinert, T. / Furrer, A. / Glover, H. / Gashi, D. / Carrillo, M. / Kondo, Y. / Stipp, R.T. / Khusainov, G. / Nass, K. / ...Authors: Wranik, M. / Kepa, M.W. / Beale, E.V. / James, D. / Bertrand, Q. / Weinert, T. / Furrer, A. / Glover, H. / Gashi, D. / Carrillo, M. / Kondo, Y. / Stipp, R.T. / Khusainov, G. / Nass, K. / Ozerov, D. / Cirelli, C. / Johnson, P.J.M. / Dworkowski, F. / Beale, J.H. / Stubbs, S. / Zamofing, T. / Schneider, M. / Krauskopf, K. / Gao, L. / Thorn-Seshold, O. / Bostedt, C. / Bacellar, C. / Steinmetz, M.O. / Milne, C. / Standfuss, J.
History
DepositionFeb 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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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)253,95122
Polymers249,8686
Non-polymers4,08216
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23150 Å2
ΔGint-165 kcal/mol
Surface area83400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.760, 160.760, 180.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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


Mass: 48966.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 48391.410 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q6B856
#3: Protein Stathmin-4


Mass: 14536.567 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#4: Protein Tubulin-Tyrosine Ligase


Mass: 40616.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 8 types, 60 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.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-EP / EPOTHILONE A


Mass: 493.656 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C26H39NO6S / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-LOC / N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide / COLCHICINE


Mass: 399.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25NO6 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antiinflammatory*YM
#10: 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
#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.: 44 / 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: 3.12 Å3/Da / Density % sol: 60.52 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 6.5
Details: 6% PEG4000 (w/v), 30 mM MgCl2, 30 mM CaCl2, 0.1 M MES/Imidazole, 5 mM L-tyrosine

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1.03 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.6→15.26 Å / Num. obs: 95755 / % possible obs: 100 % / Redundancy: 209.7 % / CC1/2: 0.983 / Net I/σ(I): 4.72
Reflection shellResolution: 2.6→2.7 Å / Mean I/σ(I) obs: 0.89 / Num. unique obs: 9439 / CC1/2: 0.37
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: Hydroxyethylcellulose / Description: High-viscosity injection / Injector diameter: 75 µm

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Processing

Software
NameVersionClassification
PHENIX1.20_4487refinement
CrystFEL0.8.0data reduction
CrystFEL0.8.0data scaling
PHENIX1.20_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→15.26 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2267 1427 1.86 %
Rwork0.1782 --
obs0.1791 76658 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→15.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17488 0 256 44 17788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.353
X-RAY DIFFRACTIONf_dihedral_angle_d11.1132667
X-RAY DIFFRACTIONf_chiral_restr0.0732773
X-RAY DIFFRACTIONf_plane_restr0.0113313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90.30911410.2717399X-RAY DIFFRACTION100
2.9-3.010.29421410.26267483X-RAY DIFFRACTION100
3.01-3.150.27711420.24187465X-RAY DIFFRACTION100
3.15-3.320.25361410.21937452X-RAY DIFFRACTION100
3.32-3.520.2821420.19637480X-RAY DIFFRACTION100
3.52-3.790.22351420.17777505X-RAY DIFFRACTION100
3.79-4.160.20581430.15747509X-RAY DIFFRACTION100
4.16-4.750.18291430.14037575X-RAY DIFFRACTION100
4.75-5.920.21681450.15717623X-RAY DIFFRACTION100
5.92-15.260.20881470.16147740X-RAY DIFFRACTION99
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)
11.47140.1184-0.18482.40330.46192.30680.08580.03960.1768-0.20920.0603-0.1838-0.35320.2009-0.11530.3573-0.00660.03010.3747-0.13130.401429.268887.766255.9131
21.72651.1083-0.66842.43421.61366.04390.2752-0.04540.28670.1711-0.06020.5424-0.3356-0.5928-0.16650.39780.01690.12250.4249-0.14050.5339.621486.818871.7206
30.9353-0.718-0.44993.5991.33282.7737-0.0942-0.057-0.06220.65830.07640.17760.22730.1271-0.00160.2677-0.0120.01790.2997-0.09840.379423.449678.85970.0677
41.8611-0.4851-0.41152.13711.02322.36950.03330.09520.2266-0.4023-0.08510.0977-0.4505-0.1545-0.00520.37060.0208-0.01760.3395-0.11520.350619.355761.548721.5125
55.308-1.07780.78163.7539-0.5322.84010.0742-0.02510.1316-0.2124-0.05350.3367-0.3042-0.43720.01530.40530.0822-0.01380.4052-0.19010.39469.245164.504637.4045
61.0272-0.28220.43592.07011.27072.8309-0.0762-0.23850.15840.293-0.08880.10010.1501-0.38540.08340.2371-0.04120.01480.3632-0.0990.344814.144252.092238.4302
74.1669-1.4546-1.13344.4564-0.40382.3416-0.07220.24060.46960.02670.0410.4137-0.535-0.154-0.01520.3889-0.0224-0.01390.26850.00470.330114.260643.618-13.2439
81.90270.1404-0.32882.26670.12511.87070.04480.11670.0374-0.17060.021-0.0207-0.11170.1157-0.0570.2588-0.04440.01390.2454-0.03980.252117.593229.6393-8.6551
91.8176-0.74310.46211.90760.06921.5459-0.0424-0.11260.00410.0969-0.06790.23920.0185-0.23140.09340.255-0.05340.02690.3002-0.07030.28333.59829.23366.1673
102.9245-1.5499-2.64472.85353.03986.2268-0.1996-0.2254-0.34930.49530.1906-0.23490.92050.633-0.12870.36370.0149-0.06070.3174-0.01540.399525.640812.88172.3872
115.0282-1.95450.22754.1345-0.35231.9921-0.05510.68530.1846-0.68150.09480.0194-0.0343-0.3001-0.10180.7106-0.09940.05290.7905-0.08560.386217.046910.3864-44.0328
121.9952-0.0793-0.35951.71180.02781.5964-0.10820.4411-0.3674-0.41280.2059-0.21510.23090.0392-0.05110.539-0.08790.1070.6052-0.21330.468223.058-2.0407-35.888
132.1681-0.3493-0.48322.00970.4132.0803-0.08270.2911-0.2086-0.06210.0430.14710.2884-0.27240.00110.4117-0.07730.02580.3767-0.11280.38837.9433-1.7622-22.0611
144.9792-1.543-3.07472.06050.74475.104-0.3668-0.2159-0.55260.40690.2233-0.1670.9740.6979-0.08760.58840.04220.01950.5453-0.21070.719430.4032-16.3994-24.3159
158.0817-0.01190.8997.6777-6.18698.4497-0.2471-0.14880.2942-0.0957-0.3912-0.2031-0.37790.20330.41240.7111-0.14660.0750.6145-0.28720.586325.8775101.57681.9371
160.01470.12890.04131.12440.34940.1080.0004-0.0211-0.38840.765-0.0194-0.53290.75380.98470.09161.07930.2926-0.18071.0015-0.13860.577332.444784.689282.3118
170.19230.0093-0.02380.34760.5050.47-0.20130.0354-0.00150.50060.4437-0.19290.5470.7406-0.44860.53390.07810.03620.6907-0.21220.670143.000428.99063.5893
183.18640.6667-1.23664.86040.9514.4423-0.44970.4668-0.6818-0.27010.3746-0.15041.4152-0.66770.1250.8913-0.12170.11090.5973-0.15260.65876.196956.715469.5057
196.7077-0.19091.70633.6543-1.70134.6101-0.1823-0.9565-0.150.3248-0.0978-0.8096-0.24371.05570.18230.63620.0771-0.05630.89650.05290.694516.444866.282799.9977
208.90130.11041.09976.44-2.16218.2451-0.2282-1.1656-0.42620.71460.173-1.06580.5431.13880.08621.05040.3729-0.04231.40620.16391.197716.426856.4287110.2575
211.99760.1086-0.33392.1734-1.12085.1005-0.2829-0.495-0.75180.4154-0.0238-0.41780.8360.75620.19080.92620.23530.14890.6030.17090.81275.551555.290798.9008
223.3059-1.11780.17610.61780.7432.6822-0.4244-0.3665-1.540.2320.3111-0.25091.43650.25250.1961.9970.1126-0.01331.17090.25211.70685.074341.2358105.0421
231.9379-0.1302-1.64251.6806-0.28643.5307-0.43050.1652-0.53070.13790.25780.2160.6771-0.25570.10820.7531-0.01840.08650.44240.0260.6617-3.879659.524890.7464
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 273 )
2X-RAY DIFFRACTION2chain 'A' and (resid 274 through 311 )
3X-RAY DIFFRACTION3chain 'A' and (resid 312 through 439 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 238 )
5X-RAY DIFFRACTION5chain 'B' and (resid 239 through 295 )
6X-RAY DIFFRACTION6chain 'B' and (resid 296 through 438 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 72 )
8X-RAY DIFFRACTION8chain 'C' and (resid 73 through 259 )
9X-RAY DIFFRACTION9chain 'C' and (resid 260 through 401 )
10X-RAY DIFFRACTION10chain 'C' and (resid 402 through 440 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 88 )
12X-RAY DIFFRACTION12chain 'D' and (resid 89 through 251 )
13X-RAY DIFFRACTION13chain 'D' and (resid 252 through 399 )
14X-RAY DIFFRACTION14chain 'D' and (resid 400 through 441 )
15X-RAY DIFFRACTION15chain 'E' and (resid 6 through 20 )
16X-RAY DIFFRACTION16chain 'E' and (resid 21 through 46 )
17X-RAY DIFFRACTION17chain 'E' and (resid 47 through 143 )
18X-RAY DIFFRACTION18chain 'F' and (resid 1 through 66 )
19X-RAY DIFFRACTION19chain 'F' and (resid 67 through 134 )
20X-RAY DIFFRACTION20chain 'F' and (resid 135 through 165 )
21X-RAY DIFFRACTION21chain 'F' and (resid 166 through 223 )
22X-RAY DIFFRACTION22chain 'F' and (resid 224 through 257 )
23X-RAY DIFFRACTION23chain 'F' and (resid 258 through 378 )

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