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- PDB-8bde: Tubulin-baccatin III complex -

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Basic information

Entry
Database: PDB / ID: 8bde
TitleTubulin-baccatin III complex
Components
  • (Tubulin beta-2B ...) x 2
  • Stathmin-4
  • Tubulin alpha-1B chain
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 / microtubule-based process / cytoplasmic microtubule / 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 / microtubule-based process / cytoplasmic microtubule / tubulin binding / cellular response to interleukin-4 / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / neuron projection development / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / cilium / protein heterodimerization activity / nucleotide binding / GTPase activity / 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. / Helix hairpin bin / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. ...Rossmann fold - #11480 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Helix hairpin bin / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 60s Ribosomal Protein L30; Chain: A; / 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 / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-R3Q / 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: 1.902 Å
AuthorsProta, A.E. / Lucena-Agell, D. / Ma, Y. / Estevez-Gallego, J. / Li, S. / Bargsten, K. / Altmann, K.H. / Gaillard, N. / Kamimura, S. / Muehlethaler, T. ...Prota, A.E. / Lucena-Agell, D. / Ma, Y. / Estevez-Gallego, J. / Li, S. / Bargsten, K. / Altmann, K.H. / Gaillard, N. / Kamimura, S. / Muehlethaler, T. / Gago, F. / Oliva, M.A. / Steinmetz, M.O. / Fang, W.S. / Diaz, J.F.
Funding support Switzerland, Spain, European Union, 4items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166608 Switzerland
Spanish Ministry of Science, Innovation, and Universities2019-104545RB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesCOV20/01007 Spain
H2020 Marie Curie Actions of the European Commission2019 860070European Union
CitationJournal: Elife / Year: 2023
Title: Structural insight into the stabilization of microtubules by taxanes.
Authors: Prota, A.E. / Lucena-Agell, D. / Ma, Y. / Estevez-Gallego, J. / Li, S. / Bargsten, K. / Josa-Prado, F. / Altmann, K.H. / Gaillard, N. / Kamimura, S. / Muhlethaler, T. / Gago, F. / Oliva, M.A. ...Authors: Prota, A.E. / Lucena-Agell, D. / Ma, Y. / Estevez-Gallego, J. / Li, S. / Bargsten, K. / Josa-Prado, F. / Altmann, K.H. / Gaillard, N. / Kamimura, S. / Muhlethaler, T. / Gago, F. / Oliva, M.A. / Steinmetz, M.O. / Fang, W.S. / Diaz, J.F.
History
DepositionOct 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 beta-2B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,05320
Polymers261,6316
Non-polymers3,42214
Water15,475859
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22550 Å2
ΔGint-159 kcal/mol
Surface area79070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.100, 157.150, 179.150
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 , 2 types, 3 molecules ACE

#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
#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

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Tubulin beta-2B ... , 2 types, 3 molecules BDF

#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
#4: Protein Tubulin beta-2B chain


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, 873 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.: 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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-R3Q / [(1~{S},2~{S},3~{R},4~{S},7~{R},9~{S},10~{S},12~{R},15~{S})-4,12-diacetyloxy-10,14,16,16-tetramethyl-1,9,15-tris(oxidanyl)-11-oxidanylidene-6-oxatetracyclo[11.3.1.0^{3,10}.0^{4,7}]heptadec-13-en-2-yl] benzoate / Baccatin III / O-De[(2R,3S)-3-(Benzoylamino)-2-hydroxy-3-phenylpropanoyl]paclitaxel


Mass: 586.627 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H38O11 / Feature type: SUBJECT OF INVESTIGATION
#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.: 859 / 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: 2.98 Å3/Da / Density % sol: 58.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.7
Details: 2-4% PEG 4K, 2-10% glycerol, 30 mM MgCl2, 30 mM CaCl2, 0.1 M MES/Imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.9→49.195 Å / Num. obs: 229672 / % possible obs: 100 % / Redundancy: 13.537 % / Biso Wilson estimate: 41.71 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.111 / Χ2: 1.03 / Net I/σ(I): 16.49 / Num. measured all: 3109004 / Scaling rejects: 400
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
1.9-1.9512.4284.9190.5420854216822167800.1785.13199.8
1.95-2.0113.8823.5550.8122857816473164660.3253.69100
2.01-2.0613.7432.5891.1221880115924159210.4572.688100
2.06-2.1313.0061.9381.4620245415568155660.5792.018100
2.13-2.214.0211.4162.0821066415029150250.7291.469100
2.2-2.2714.1931.0752.7620744014619146160.8151.115100
2.27-2.3614.1270.8143.6219891614081140810.890.844100
2.36-2.4613.9290.64.8718904613574135720.9360.623100
2.46-2.5613.6830.4496.3617765812984129840.9610.466100
2.56-2.6912.7950.3288.2815953712470124690.9750.342100
2.69-2.8413.8070.24311.5316381711865118650.9880.253100
2.84-3.0113.6580.16716.2415334711229112280.9940.173100
3.01-3.2213.0890.10922.8713858810589105880.9970.114100
3.22-3.4714.2060.07433.51140244987298720.9990.077100
3.47-3.813.9760.0545.91127186910091000.9990.052100
3.8-4.2513.4420.03858.311112158275827410.039100
4.25-4.9112.410.02967.1910767339733910.031100
4.91-6.0213.2820.0368.39827216230622810.032100
6.02-8.5112.9450.02676.42634164900489910.027100
8.51-49.19512.7750.02194.91357582823279910.02299.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5lxt

5lxt


Resolution: 1.902→49.195 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2177 1999 87 %
Rwork0.1919 227655 -
obs0.1921 229654 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 199.37 Å2 / Biso mean: 58.9316 Å2 / Biso min: 23.8 Å2
Refinement stepCycle: final / Resolution: 1.902→49.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17246 0 212 859 18317
Biso mean--64.12 56.15 -
Num. residues----2178
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9021-1.94970.38541400.407116032
1.9497-2.00240.3381420.350616141
2.0024-2.06130.33211410.316116084
2.0613-2.12780.31451420.291116184
2.1278-2.20390.2911420.261816131
2.2039-2.29210.26161420.235516162
2.2921-2.39640.24851420.223416176
2.3964-2.52280.2341430.211116230
2.5228-2.68080.23211420.20516233
2.6808-2.88780.23991420.205516259
2.8878-3.17840.21481440.196516281
3.1784-3.63820.20141430.180416357
3.6382-4.58320.19841450.148216489
4.5832-49.1950.17791490.165116896
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)
10.8005-0.2307-0.67860.9013-0.44611.06950.05250.08720.1551-0.35150.139-0.1151-0.69120.10980.00010.6874-0.04720.06490.3731-0.09410.411927.955695.766251.3244
20.4508-0.5474-0.20740.90750.54421.2524-0.03210.1638-0.075-0.24320.2807-0.2821-0.27820.43570.00120.3628-0.09560.10140.4322-0.18290.405337.153880.680750.2948
30.2296-0.1674-0.25330.59240.00990.233-0.0566-0.0937-0.01120.24910.1208-0.09510.11470.21090.00010.37720.00650.00120.3915-0.14730.382730.195973.67759.0986
40.8378-0.5561-0.66011.37050.20912.05470.09080.00360.04350.2392-0.01260.0157-0.19360.046800.34350.02060.02520.3068-0.09830.37720.98583.831964.5873
50.23590.1863-0.04310.2980.1630.31950.2328-0.0533-0.16690.4514-0.28320.68380.1741-0.3005-0.03550.51030.01160.13650.4848-0.17420.56399.155783.80171.7041
60.38880.18420.07711.73810.89861.64470.0016-0.09810.00550.51230.02730.03060.17660.0599-0.00010.42050.01540.04210.3249-0.08130.326323.159476.501969.7439
71.75080.23390.40920.7981-0.00361.17210.09660.28340.296-0.3398-0.13560.1269-0.43480.0036-00.39840.02050.01590.3406-0.02110.360520.090265.342817.9709
80.7346-0.006-0.05491.32230.86912.40820.0257-0.11320.06180.1142-0.11460.1092-0.0631-0.1641-0.01110.22750.0060.0380.3255-0.11650.356118.037655.428428.6206
90.6431-0.18480.49050.97390.12421.3499-0.2174-0.216-0.16350.2705-0.03040.30.0875-0.7133-0.00040.39570.04930.0660.64-0.19520.47275.308358.69441.846
100.661-0.09880.89480.22030.17671.4888-0.0168-0.12520.11150.3476-0.10680.04720.0976-0.4174-0.00740.3314-0.04480.11740.3963-0.09560.367212.475851.245739.1889
110.24170.35770.12260.70560.07730.18930.13-0.0599-0.29860.40190.0001-0.2140.52950.4450.00130.394-0.0223-0.05240.3629-0.03670.330326.005937.515930.8862
120.99240.0157-0.08291.180.24841.2961-0.03840.09940.0678-0.13990.0930.0067-0.08670.04600.2402-0.0370.02460.3066-0.03890.300117.367131.4877-10.8965
130.9542-0.41470.12291.43721.09131.3513-0.0267-0.06540.0980.1437-0.03620.04960.1359-0.1691-0.00010.2483-0.06140.04890.2909-0.02210.3078.749625.47445.3316
140.62890.05920.36780.28890.18990.2801-0.17940.61410.1188-0.36160.14460.07750.0381-0.148900.5109-0.08690.02540.6826-0.04340.391515.318111.5906-41.1989
151.0129-0.1588-0.11350.7775-0.26610.7726-0.11350.7060.167-0.42060.2389-0.28370.05650.2660.01490.5316-0.0660.13370.7522-0.20160.410127.94893.7196-44.9031
160.9910.1438-0.23070.9829-0.15361.2667-0.10670.2941-0.156-0.22370.1359-0.14440.29880.076-0.00480.4245-0.03350.04590.4431-0.17680.376619.8516-3.7981-31.8486
171.39-0.3933-0.06620.95550.19721.6636-0.12460.2257-0.21630.00990.04610.20370.2642-0.3194-0.00010.4501-0.10340.01920.4396-0.10940.4137.1841-3.0676-22.4997
180.861-0.22860.14081.06330.25590.7973-0.12430.1341-1.01480.28050.024-0.09381.10120.14070.33690.64690.17530.02770.4207-0.35470.663730.5258-17.3378-25.0957
190.48070.32340.31760.42890.41950.3638-0.0639-0.07470.26990.26480.0964-0.3609-0.1450.4734-0.0010.87440.0244-0.03460.5198-0.15430.52627.569492.333681.798
20-0.0045-0.1063-0.2268-0.0590.09370.18920.009-0.0215-0.04550.33170.443-0.45340.39660.57380.02570.39190.06550.01530.6122-0.26950.552743.043728.63154.7347
211.0457-0.1368-1.02280.40610.33090.978-0.44650.4323-0.3933-0.08560.1155-0.21410.7831-0.2218-0.03160.8893-0.1270.13470.5198-0.15450.54626.433954.161569.9088
220.0756-0.04380.06250.0746-0.0010.07030.0528-0.61410.33480.2471-0.0444-0.32830.08640.83490.00010.73240.0229-0.00490.8947-0.01010.611811.03665.514397.424
230.06460.01860.05470.01950.05420.06140.0601-0.5603-0.35460.4447-0.2904-0.74720.56331.1831-0.00020.93560.2593-0.10181.56980.22620.989620.800956.4417107.6099
241.36680.0649-0.72030.2030.18970.5233-0.4552-0.0515-0.49910.05450.0368-0.0360.8226-0.0142-0.00270.86530.04640.15320.41570.11920.607-1.976752.870696.9176
250.5095-0.6202-0.12630.9513-0.30820.8987-0.46120.0545-1.10910.22410.0712-0.09451.1487-0.0263-1.05291.30830.18010.34260.44080.20391.0876-1.933943.7561104.1102
261.7868-0.3063-1.33270.20690.0621.1344-0.23230.1384-0.2660.02460.2311-0.07570.41040.0144-0.00020.7539-0.02070.06950.45460.00340.4916-0.99359.547587.4011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 88 )A1 - 88
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 160 )A89 - 160
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 199 )A161 - 199
4X-RAY DIFFRACTION4chain 'A' and (resid 200 through 273 )A200 - 273
5X-RAY DIFFRACTION5chain 'A' and (resid 274 through 311 )A274 - 311
6X-RAY DIFFRACTION6chain 'A' and (resid 312 through 437 )A312 - 437
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 127 )B1 - 127
8X-RAY DIFFRACTION8chain 'B' and (resid 128 through 259 )B128 - 259
9X-RAY DIFFRACTION9chain 'B' and (resid 260 through 338 )B260 - 338
10X-RAY DIFFRACTION10chain 'B' and (resid 339 through 401 )B339 - 401
11X-RAY DIFFRACTION11chain 'B' and (resid 402 through 438 )B402 - 438
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 243 )C1 - 243
13X-RAY DIFFRACTION13chain 'C' and (resid 244 through 440 )C244 - 440
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 56 )D1 - 56
15X-RAY DIFFRACTION15chain 'D' and (resid 57 through 140 )D57 - 140
16X-RAY DIFFRACTION16chain 'D' and (resid 141 through 268 )D141 - 268
17X-RAY DIFFRACTION17chain 'D' and (resid 269 through 399 )D269 - 399
18X-RAY DIFFRACTION18chain 'D' and (resid 400 through 441 )D400 - 441
19X-RAY DIFFRACTION19chain 'E' and (resid 6 through 46 )E6 - 46
20X-RAY DIFFRACTION20chain 'E' and (resid 47 through 141 )E47 - 141
21X-RAY DIFFRACTION21chain 'F' and (resid 1 through 66 )F1 - 66
22X-RAY DIFFRACTION22chain 'F' and (resid 67 through 96 )F67 - 96
23X-RAY DIFFRACTION23chain 'F' and (resid 97 through 184 )F97 - 184
24X-RAY DIFFRACTION24chain 'F' and (resid 185 through 223 )F185 - 223
25X-RAY DIFFRACTION25chain 'F' and (resid 224 through 283 )F224 - 283
26X-RAY DIFFRACTION26chain 'F' and (resid 284 through 380 )F284 - 380

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