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- PDB-8clf: Z-SolQ2Br bound to tubulin (T2R-TTL) complex -

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Basic information

Entry
Database: PDB / ID: 8clf
TitleZ-SolQ2Br 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
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 ...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-V1O / 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: 2.7 Å
AuthorsWranik, M. / Bertrand, Q. / Kepa, M. / 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)249,24718
Polymers246,2376
Non-polymers3,01112
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21390 Å2
ΔGint-152 kcal/mol
Surface area81550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.650, 160.330, 180.950
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: 14336.375 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: 37184.664 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 , 7 types, 42 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: isolated from a natural source / Formula: Mg
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / 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-V1O / 5-[[4-(2-bromoethyl)-3,5-dimethoxy-phenyl]diazenyl]-2-methoxy-phenol


Mass: 395.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19BrN2O4 / 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.: 30 / 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: 3.15 Å3/Da / Density % sol: 60.94 %
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→15.35 Å / Num. obs: 95765 / % possible obs: 100 % / Redundancy: 381.3 % / CC1/2: 0.976 / Net I/σ(I): 6.13
Reflection shellResolution: 2.6→2.7 Å / Mean I/σ(I) obs: 0.59 / Num. unique obs: 9439 / CC1/2: 0.25
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: 2.7→15.35 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2169 1481 1.74 %
Rwork0.168 --
obs0.1689 85178 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→15.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17237 0 181 30 17448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.864
X-RAY DIFFRACTIONf_dihedral_angle_d5.2522564
X-RAY DIFFRACTIONf_chiral_restr0.112698
X-RAY DIFFRACTIONf_plane_restr0.0043263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.790.37411330.30777534X-RAY DIFFRACTION100
2.79-2.890.35531340.29857540X-RAY DIFFRACTION100
2.89-30.33131330.26497534X-RAY DIFFRACTION100
3-3.140.34161340.25477558X-RAY DIFFRACTION100
3.14-3.30.25391330.20687530X-RAY DIFFRACTION100
3.3-3.50.25731340.17657597X-RAY DIFFRACTION100
3.5-3.770.22171340.15427583X-RAY DIFFRACTION100
3.77-4.140.20091350.13937601X-RAY DIFFRACTION100
4.14-4.730.17291350.12287662X-RAY DIFFRACTION100
4.73-5.90.1631370.14567716X-RAY DIFFRACTION100
5.9-15.350.19291390.15417842X-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)
11.58680.1343-0.07663.33340.60222.54380.05840.06730.2094-0.20660.228-0.3539-0.49360.2887-0.27680.5704-0.04610.0760.5817-0.15830.613729.345687.673955.9811
22.13382.13220.17662.98711.17147.16620.3114-0.03670.42760.21-0.0151.1922-0.7411-0.7109-0.22670.51330.07810.17060.5988-0.11380.77849.762986.501671.82
31.7984-1.0513-0.83335.49172.18034.1428-0.0347-0.03810.03280.81410.13450.13640.19040.212-0.10.43950.0219-0.00340.5121-0.13320.550423.559478.779270.1417
42.5491-0.6023-0.35792.60990.68522.92480.07010.1290.2279-0.3767-0.09620.0083-0.4383-0.13510.01270.47620.02430.01140.4935-0.10760.475619.393861.639121.7921
55.5537-0.28130.14825.40110.12332.45330.09410.1557-0.2013-0.2402-0.05320.7156-0.1243-0.5791-0.05760.5110.02740.03610.6948-0.23010.51858.952860.725538.2614
61.307-0.66740.50773.24192.21014.3501-0.1066-0.2520.13680.51650.04270.05740.3156-0.35660.09160.3746-0.09050.07270.5252-0.04710.489515.450852.039738.1112
71.73490.0012-0.20152.3604-0.17621.55790.00290.19630.1701-0.2011-0.00350.0825-0.1760.00060.00610.4499-0.03780.01370.4772-0.03110.416416.943633.1498-9.911
81.4011-0.43480.03421.90220.76331.745-0.0952-0.11240.05040.1862-0.03880.10660.1649-0.20530.13790.3815-0.0710.02260.418-0.04620.39928.387825.38895.3858
94.0078-0.7599-0.05873.38330.55383.4582-0.1590.58610.2513-0.79490.08110.011-0.1961-0.26240.00970.9153-0.1468-0.02460.947-0.00850.482115.682212.7832-41.7174
102.0143-0.391-0.02482.70430.09772.3923-0.37751.0202-0.2561-1.01890.3363-0.53880.41840.3427-0.07131.1168-0.21860.26751.2105-0.30320.703529.67330.8703-46.5275
113.12730.6238-0.08492.0863-0.84232.4452-0.1370.3709-0.4511-0.43430.2352-0.39550.33660.4526-0.00780.7558-0.08210.14950.7844-0.26710.590327.2876-0.1734-34.1684
122.85690.1143-0.07882.368-0.08632.7111-0.13790.5159-0.3798-0.48220.04320.04870.5459-0.3861-0.00721.0167-0.18690.11660.8107-0.27260.663215.4994-9.255-34.2332
132.08880.61491.86072.4654-2.03665.7006-0.30.3650.09150.07990.3873-0.098-0.322-0.0521-0.16010.5434-0.06090.13930.5907-0.15850.587817.03585.3898-23.4267
142.9351-1.1785-1.67814.35291.68681.52920.2980.8332-0.8069-1.0859-0.35740.72390.2001-0.44270.13850.9951-0.1935-0.03260.948-0.25350.876-0.0174-5.3368-26.2515
153.6593-1.2124-0.37133.60610.32172.4744-0.30480.3715-0.2544-0.0060.14190.15210.3215-0.35780.10120.5258-0.18870.04160.4915-0.10310.4589.4169-2.2146-20.9943
164.5949-1.6283-1.02384.03590.32652.6486-0.2096-0.0264-0.9092-0.12370.1756-0.31330.8770.6999-0.22590.82660.00140.05080.6901-0.27290.895130.4205-15.9435-23.7862
173.97590.28241.12925.6635-0.78653.52990.1875-0.52140.35430.7282-0.4738-0.1833-0.38560.37660.21110.8762-0.0654-0.0820.867-0.10170.73928.562294.34882.2109
180.2316-0.0907-0.27066.20916.39466.6481-0.15680.016-0.00640.44920.3508-0.14620.55970.6194-0.35340.68480.0720.07430.8323-0.18710.820743.123729.87314.8171
196.49481.3442-1.14446.20850.70747.6786-0.4050.4051-0.8135-0.31160.3442-0.0651.5685-0.31340.08491.0574-0.08940.15590.6731-0.14180.6986.577256.452769.7073
204.24280.955-0.54123.2219-1.28645.1446-0.1577-0.8691-0.75450.5265-0.1398-0.54990.68610.87040.20040.91720.25540.08550.75110.13410.729510.159859.7838100.9887
210.50320.9359-0.681.8318-1.6152.0665-0.41420.0903-1.41450.14230.1359-1.16791.91830.91470.49822.14530.33460.2221.31290.18822.0345.162741.1002103.9036
222.80930.2856-2.16611.7855-0.53084.4959-0.49220.1645-0.44410.2180.37070.21090.8803-0.36960.04480.8719-0.0050.13270.48660.04460.6697-3.39659.089390.9927
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 243 )
5X-RAY DIFFRACTION5chain 'B' and (resid 244 through 311 )
6X-RAY DIFFRACTION6chain 'B' and (resid 312 through 438 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 259 )
8X-RAY DIFFRACTION8chain 'C' and (resid 260 through 440 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 64 )
10X-RAY DIFFRACTION10chain 'D' and (resid 65 through 127 )
11X-RAY DIFFRACTION11chain 'D' and (resid 128 through 180 )
12X-RAY DIFFRACTION12chain 'D' and (resid 181 through 238 )
13X-RAY DIFFRACTION13chain 'D' and (resid 239 through 273 )
14X-RAY DIFFRACTION14chain 'D' and (resid 274 through 311 )
15X-RAY DIFFRACTION15chain 'D' and (resid 312 through 401 )
16X-RAY DIFFRACTION16chain 'D' and (resid 402 through 441 )
17X-RAY DIFFRACTION17chain 'E' and (resid 6 through 46 )
18X-RAY DIFFRACTION18chain 'E' and (resid 47 through 141 )
19X-RAY DIFFRACTION19chain 'F' and (resid 1 through 66 )
20X-RAY DIFFRACTION20chain 'F' and (resid 67 through 223 )
21X-RAY DIFFRACTION21chain 'F' and (resid 224 through 257 )
22X-RAY DIFFRACTION22chain 'F' and (resid 258 through 378 )

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