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- PDB-8clc: Tubulin (T2R-TTL) complex -

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Basic information

Entry
Database: PDB / ID: 8clc
TitleTubulin (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 / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / 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.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)250,06916
Polymers247,4786
Non-polymers2,59110
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21540 Å2
ΔGint-136 kcal/mol
Surface area82490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.530, 160.480, 181.240
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: 48260.215 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) / Gene: Stmn4 / Production host: Escherichia coli (E. coli)
#4: Protein Tubulin-Tyrosine Ligase


Mass: 38487.980 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 , 6 types, 101 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.: 3 / Source method: obtained synthetically / 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-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
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.14 Å3/Da / Density % sol: 60.88 %
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: 2.4→15.22 Å / Num. obs: 121578 / % possible obs: 100 % / Redundancy: 185.5 % / CC1/2: 0.951 / Net I/σ(I): 3.88
Reflection shellResolution: 2.4→2.5 Å / Mean I/σ(I) obs: 0.41 / Num. unique obs: 12016 / CC1/2: 0.19
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: Hydroxyethylcellulose / Description: High-viscosity injectio / 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→15.2 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2344 627 0.74 %
Rwork0.1864 --
obs0.1868 85293 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→15.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17281 0 156 91 17528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.462
X-RAY DIFFRACTIONf_dihedral_angle_d10.7262438
X-RAY DIFFRACTIONf_chiral_restr0.042642
X-RAY DIFFRACTIONf_plane_restr0.0043146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.970.31751560.297420959X-RAY DIFFRACTION100
2.97-3.40.31081550.243920985X-RAY DIFFRACTION100
3.4-4.260.2121560.175221158X-RAY DIFFRACTION100
4.26-15.20.20831600.153521564X-RAY DIFFRACTION100
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)
11.85610.2221-0.11352.89430.78052.49590.04310.05560.1399-0.260.1559-0.2622-0.4730.2314-0.19270.4622-0.04230.06120.491-0.14250.496729.201287.741455.88
21.60821.8141-0.09922.63530.11747.55710.1056-0.0436-0.06440.2505-0.03840.9546-0.3797-0.5461-0.07220.47510.04750.0760.5713-0.17640.71379.506486.697471.6658
30.9972-0.3287-0.6283.38661.43023.0717-0.0533-0.0843-0.02690.53960.06840.18630.1820.1219-0.01660.35970.0225-0.03750.459-0.08550.43523.441178.773870.0284
44.434-1.4201-0.044.12280.37613.81510.00120.16950.6781-0.5368-0.01580.1334-0.9-0.24290.01540.76120.0653-0.00170.5237-0.02470.642815.596874.062321.9574
51.6891-0.9677-0.43065.18280.73773.2330.07510.25220.2136-0.6197-0.0993-0.0424-0.54030.0446-0.01140.5334-0.01290.03240.5393-0.05620.469124.661161.836713.1884
61.3274-0.69160.42152.79210.93152.6736-0.0558-0.0568-0.0108-0.1587-0.08530.0853-0.0935-0.22420.11110.32470.02810.01540.4641-0.12580.416317.817954.930226.0848
73.0936-1.72642.73311.133-1.81152.9712-0.1399-0.35820.25640.14120.13810.2594-0.5723-0.17860.01040.58740.02680.03260.5742-0.15920.610519.715170.213938.0116
82.8857-0.7090.85152.51740.15262.8648-0.226-0.26180.00450.1517-0.05820.3567-0.1088-0.77710.21160.40530.03590.01840.6782-0.20140.51526.605461.95742.3639
90.6329-0.2184-0.18351.16681.87563.0355-0.2436-0.1448-0.0090.4630.0230.27140.4161-0.09670.24020.4624-0.00830.02360.594-0.08520.507815.016545.020434.0725
101.7170.1214-0.24343.53362.07297.3041-0.1526-0.1924-0.24570.59150.1351-0.15620.65890.5317-0.00320.43540.0584-0.0410.4318-0.0350.454725.607340.180431.8816
113.1273-0.4761-0.11963.8232-0.24862.092-0.02990.16140.4911-0.2093-0.03140.2378-0.3343-0.11650.03460.5217-0.0497-0.01650.49420.03330.473314.32243.4689-13.2604
121.7612-0.10390.1152.34240.06261.85070.00790.12770.0495-0.22780.0084-0.0072-0.10690.0567-0.01560.3712-0.03380.01030.4155-0.02870.373817.691429.4266-8.643
131.5086-0.24680.12111.64120.61.6692-0.0972-0.0810.09290.1468-0.02750.0880.0878-0.19790.11210.3692-0.07210.02630.4316-0.04030.41728.285125.42925.4851
143.6626-0.8810.70252.24630.87693.0005-0.18920.76640.2988-0.67770.1035-0.01320.084-0.24570.0790.7969-0.1660.03010.8887-0.02020.447115.578212.6448-41.4487
152.6219-0.3765-0.13882.8034-0.72622.6692-0.17590.7329-0.1111-0.84660.1067-0.36670.25130.30820.06190.9057-0.17180.18910.9934-0.27470.607429.60121.3962-42.4704
163.2789-0.1978-0.02430.5845-0.78351.2847-0.04990.2597-0.5357-0.3310.0367-0.3580.42230.0644-0.00440.8214-0.09840.13420.7034-0.24290.632321.8562-8.1519-31.6685
171.8553-0.4739-0.11721.6550.46052.4495-0.14110.4784-0.3202-0.64850.08020.13880.1134-0.39230.10760.669-0.10850.04590.7476-0.13110.519811.18431.479-31.6978
183.1764-1.00930.68133.61850.78622.6040.32390.1472-0.3053-0.6189-0.26270.4770.5953-0.4794-0.13180.7028-0.18640.01510.6042-0.14550.51145.8309-2.303-25.1753
192.7786-0.2593-0.51842.14620.07671.9726-0.2760.3691-0.3862-0.07210.20830.26660.235-0.34840.13920.5447-0.13240.04510.52-0.15590.48798.4921-2.6091-20.5197
203.6669-0.683-0.84542.6658-0.38182.961-0.4024-0.0039-0.90950.20240.15-0.27420.99410.55150.12430.80890.03140.08890.6407-0.26050.864430.3451-16.7736-23.874
216.1051-0.00070.88757.4502-0.89626.9422-0.12650.0550.02670.4876-0.1727-0.2571-0.34780.44320.16620.7917-0.05750.0190.7666-0.21290.780325.6268101.29482.2625
221.02230.5740.3780.6301-0.08670.4313-0.2989-0.2174-0.46650.73620.4151-0.64960.91130.815-0.03111.14630.1358-0.10310.9068-0.24320.626132.093384.698982.2557
230.17050.32390.06063.4743.84284.2179-0.158-0.0526-0.03920.27710.632-0.46170.40.7919-0.58970.59650.04970.00770.7959-0.21520.804443.206429.00194.0433
243.26910.474-1.79643.8422-0.2213.8927-0.48620.3282-0.6394-0.15360.2292-0.09041.1449-0.31570.22960.8943-0.06890.09680.6394-0.09970.74286.489656.601969.4869
253.67340.8376-0.71272.6411-0.63943.2836-0.1084-0.9123-0.48740.5718-0.0158-0.52520.46311.03630.07520.9690.2412-0.03341.02880.14160.882413.766359.7122104.1174
260.66330.554-0.30292.745-1.8445.145-0.398-0.3741-0.7193-0.0453-0.2656-0.70051.5210.31170.75581.18990.12020.28420.88130.2451.24451.210850.445897.3257
272.4360.1508-2.21681.94880.00864.2972-0.3350.1481-0.50970.19650.31990.13410.6595-0.2039-0.0050.85340.02850.09210.57010.08550.7305-2.693358.930892.7438
284.943-3.0132-3.42053.70431.33712.7431-0.32340.5280.0284-0.20190.527-0.12280.5973-0.926-0.16790.6897-0.1393-0.04560.81370.09141.0073-7.726864.459378.7731
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 2 through 59 )
5X-RAY DIFFRACTION5chain 'B' and (resid 60 through 127 )
6X-RAY DIFFRACTION6chain 'B' and (resid 128 through 238 )
7X-RAY DIFFRACTION7chain 'B' and (resid 239 through 259 )
8X-RAY DIFFRACTION8chain 'B' and (resid 260 through 372 )
9X-RAY DIFFRACTION9chain 'B' and (resid 373 through 401 )
10X-RAY DIFFRACTION10chain 'B' and (resid 402 through 440 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 72 )
12X-RAY DIFFRACTION12chain 'C' and (resid 73 through 259 )
13X-RAY DIFFRACTION13chain 'C' and (resid 260 through 440 )
14X-RAY DIFFRACTION14chain 'D' and (resid 2 through 64 )
15X-RAY DIFFRACTION15chain 'D' and (resid 65 through 160 )
16X-RAY DIFFRACTION16chain 'D' and (resid 161 through 214 )
17X-RAY DIFFRACTION17chain 'D' and (resid 215 through 259 )
18X-RAY DIFFRACTION18chain 'D' and (resid 260 through 296 )
19X-RAY DIFFRACTION19chain 'D' and (resid 297 through 399 )
20X-RAY DIFFRACTION20chain 'D' and (resid 400 through 441 )
21X-RAY DIFFRACTION21chain 'E' and (resid 6 through 20 )
22X-RAY DIFFRACTION22chain 'E' and (resid 21 through 46 )
23X-RAY DIFFRACTION23chain 'E' and (resid 47 through 143 )
24X-RAY DIFFRACTION24chain 'F' and (resid 1 through 66 )
25X-RAY DIFFRACTION25chain 'F' and (resid 67 through 207 )
26X-RAY DIFFRACTION26chain 'F' and (resid 208 through 257 )
27X-RAY DIFFRACTION27chain 'F' and (resid 258 through 353 )
28X-RAY DIFFRACTION28chain 'F' and (resid 354 through 381 )

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