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- PDB-8clb: Colchicine bound to tubulin (T2R-TTL) complex -

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Basic information

Entry
Database: PDB / ID: 8clb
TitleColchicine 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 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / nervous system development / mitotic cell cycle / microtubule / protein heterodimerization activity ...positive regulation of axon guidance / microtubule-based process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / nervous system development / mitotic cell cycle / microtubule / protein heterodimerization activity / GTPase activity / GTP binding / metal ion binding / cytoplasm / cytosol
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-LOC / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciessynthetic construct (others)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWranik, M. / Kepa, M.W. / Bertrand, Q. / 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)249,65119
Polymers246,2376
Non-polymers3,41413
Water39622
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 area80420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.710, 160.610, 180.730
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 (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 (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, 35 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-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.: 2 / Source method: obtained synthetically / Formula: C22H25NO6 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antiinflammatory*YM
#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.: 22 / 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: 3.17 Å3/Da / Density % sol: 61.25 %
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: 2.7→15.81 Å / Num. obs: 85408 / % possible obs: 100 % / Redundancy: 138.4 % / CC1/2: 0.944 / Net I/σ(I): 4.56
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 0.64 / Num. unique obs: 8462 / CC1/2: 0.207
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: 3→15.18 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2136 1141 1.84 %
Rwork0.163 --
obs0.1639 62160 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→15.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17111 0 215 22 17348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00617989
X-RAY DIFFRACTIONf_angle_d0.76224471
X-RAY DIFFRACTIONf_dihedral_angle_d11.0182535
X-RAY DIFFRACTIONf_chiral_restr0.0472682
X-RAY DIFFRACTIONf_plane_restr0.0053210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.140.3281400.27967461X-RAY DIFFRACTION99
3.14-3.30.28941410.23597549X-RAY DIFFRACTION100
3.3-3.50.22921410.20237595X-RAY DIFFRACTION100
3.5-3.770.24241420.17247588X-RAY DIFFRACTION100
3.77-4.140.19821420.15567603X-RAY DIFFRACTION100
4.14-4.730.18951430.13397662X-RAY DIFFRACTION100
4.73-5.90.22491440.14177715X-RAY DIFFRACTION100
5.9-15.180.16121480.13787846X-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)
11.69450.0386-0.2053.11550.92072.28050.05390.05790.2226-0.27480.1816-0.3735-0.47260.2635-0.20630.408-0.04970.05430.435-0.14070.460529.18387.58955.9181
21.54681.39030.03591.90810.67287.67570.13670.0830.22760.1668-0.03290.8171-0.5683-0.3084-0.15560.40810.00840.0930.3963-0.12760.63729.726786.579971.8907
31.1608-0.7007-0.2563.9431.41552.9541-0.0504-0.117-0.06810.77570.12640.06990.22820.1996-0.08570.3659-0.00060.01710.3966-0.09360.398823.459578.735570.1351
44.068-0.9137-0.04534.27651.03063.8526-0.0072-0.08510.8117-0.4475-0.00850.4674-1.046-0.28570.00490.59880.0844-0.00530.4155-0.00140.549515.363273.73522.1871
53.0442-1.5991-0.19715.98072.02123.86120.22970.540.3332-1.223-0.47710.3613-0.826-0.50840.01720.76140.0653-0.01370.5181-0.06960.536618.091666.801312.3574
62.3256-0.4764-0.17542.79281.21133.1991-0.05070.1160.0918-0.2220.0567-0.0122-0.1677-0.0144-0.03990.29510.00230.00470.3758-0.08830.315520.68455.479823.0623
73.5586-1.78422.87253.0759-1.48974.4385-0.1577-0.49240.81420.0120.3015-0.1602-0.70570.1282-0.01260.5223-0.00370.07150.5371-0.1680.582418.7570.902438.2249
81.70870.0520.6092.57410.78012.6651-0.099-0.31210.07170.0839-0.12540.4162-0.1116-0.73710.25890.35290.05320.03310.6631-0.21270.50546.539361.484242.7677
90.7216-0.41990.27592.6911.58393.4416-0.0505-0.1627-0.09160.4080.0843-0.11410.58460.1084-0.09940.33040.01540.00210.3761-0.01270.349521.45141.722632.4108
103.2215-0.8393-0.50494.2417-0.01842.4478-0.1010.20210.3795-0.14710.05590.2952-0.4361-0.15330.00140.4094-0.0226-0.01620.39240.01310.349414.228443.5971-13.3571
112.31-1.2260.03945.1646-0.51722.47690.13880.81470.0797-1.2095-0.11410.0004-0.2363-0.01130.00930.5399-0.03430.00120.58650.00090.439218.239732.5622-22.6843
121.6915-0.1513-0.16164.1060.26162.2705-0.05730.1081-0.0688-0.24440.0114-0.3058-0.01990.31230.03550.2185-0.05020.00230.335-0.03790.265924.952627.566-7.7672
131.4036-0.75660.43321.42410.50972.2580.089-0.0331-0.1289-0.0216-0.11320.25560.1059-0.36110.10330.2891-0.04890.03860.3767-0.06390.39963.366929.62090.4715
142.3048-0.58981.30212.0560.17232.5566-0.1738-0.22510.05090.1284-0.03040.2301-0.1471-0.33530.06920.3298-0.04190.03070.4727-0.07620.42940.886336.3098.6384
151.4526-0.5328-0.23942.00920.88842.0914-0.0492-0.0826-0.20050.22440.0411-0.10910.33280.2674-0.07610.32720.00680.0010.2952-0.01740.365920.105114.52972.6979
162.8921-0.6150.1192.265-0.47891.6022-0.04310.61380.1624-0.63790.1446-0.1985-0.0335-0.0147-0.09280.782-0.14220.10510.8742-0.13590.373622.27147.3608-44.2397
171.96090.0452-0.6211.3022-0.31792.3528-0.26850.2541-0.3885-0.30290.1869-0.21430.330.206-0.00470.6345-0.05040.09390.6486-0.24110.551424.6331-3.8479-33.1692
183.00550.4130.5561.31710.73243.5867-0.13420.4923-0.2137-0.38750.27360.09860.2019-0.3083-0.1140.4623-0.12670.08250.6318-0.08360.396713.26191.2973-29.7789
191.8941-0.4639-0.50112.55160.96892.7289-0.25910.2903-0.2853-0.03080.1460.20280.3561-0.37160.13480.507-0.14510.0390.5105-0.11150.51287.8482-2.9597-21.8391
203.8185-0.5039-2.05012.60840.27692.7799-0.23560.1438-0.6490.01390.0669-0.32610.88360.3740.00990.62970.0610.0560.6431-0.21540.778130.4869-15.486-24.0908
213.30510.47960.22523.1168-3.66234.69530.0014-0.27490.23960.887-0.2433-0.3521-0.29280.76490.06530.978-0.1220.05480.8293-0.21590.64825.704498.262483.6429
220.0388-0.0076-0.01690.00030.01160.0654-0.13270.7323-0.64530.61730.3037-0.66691.7741-0.96130.09621.5637-0.0323-0.30151.3232-0.22971.441939.848979.249576.287
230.2242-0.076-0.2090.66321.06631.5365-0.0558-0.0278-0.03340.37980.3775-0.35750.52190.5966-0.42550.49750.05330.0670.6848-0.20340.642742.919729.91814.6651
243.50430.8909-1.54253.79030.50894.4687-0.16320.574-0.7646-0.26290.192-0.37641.361-0.3883-0.04020.9225-0.07890.07450.6344-0.16360.66236.197856.586869.7534
252.62720.289-1.03972.7431-0.91493.5111-0.2793-0.8539-0.43480.5439-0.0494-0.58070.56120.80330.23990.85730.21320.04240.75710.09160.748910.536260.3916101.1518
260.4435-0.1057-0.08110.7157-0.39830.3002-0.3694-0.1732-1.05440.25430.1808-0.69471.22380.88010.31071.7010.36980.20281.25050.22971.59215.581443.6784103.4404
272.17350.1469-1.29340.9339-0.16411.5235-0.36540.16-0.45150.18740.29090.23240.8799-0.2319-0.0250.9503-0.01790.14790.46140.0650.6323-3.525357.898591.7911
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 59 )
5X-RAY DIFFRACTION5chain 'B' and (resid 60 through 88 )
6X-RAY DIFFRACTION6chain 'B' and (resid 89 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 438 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 72 )
11X-RAY DIFFRACTION11chain 'C' and (resid 73 through 102 )
12X-RAY DIFFRACTION12chain 'C' and (resid 103 through 199 )
13X-RAY DIFFRACTION13chain 'C' and (resid 200 through 311 )
14X-RAY DIFFRACTION14chain 'C' and (resid 312 through 372 )
15X-RAY DIFFRACTION15chain 'C' and (resid 373 through 440 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 127 )
17X-RAY DIFFRACTION17chain 'D' and (resid 128 through 214 )
18X-RAY DIFFRACTION18chain 'D' and (resid 215 through 268 )
19X-RAY DIFFRACTION19chain 'D' and (resid 269 through 401 )
20X-RAY DIFFRACTION20chain 'D' and (resid 402 through 441 )
21X-RAY DIFFRACTION21chain 'E' and (resid 6 through 25 )
22X-RAY DIFFRACTION22chain 'E' and (resid 26 through 46 )
23X-RAY DIFFRACTION23chain 'E' and (resid 47 through 141 )
24X-RAY DIFFRACTION24chain 'F' and (resid 1 through 66 )
25X-RAY DIFFRACTION25chain 'F' and (resid 67 through 218 )
26X-RAY DIFFRACTION26chain 'F' and (resid 219 through 249 )
27X-RAY DIFFRACTION27chain 'F' and (resid 250 through 378 )

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