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- PDB-5sbc: Tubulin-maytansinoid-5a-complex -

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Basic information

Entry
Database: PDB / ID: 5sbc
TitleTubulin-maytansinoid-5a-complex
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin-Tyrosine Ligase
KeywordsCELL CYCLE / TUBULIN FOLD / CYTOSKELETON / MICROTUBULE
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic cell cycle / nervous system development / growth cone / microtubule / neuron projection / protein heterodimerization activity / GTPase activity / nucleotide binding / GTP binding / Golgi apparatus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. ...Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / 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
Chem-5JS / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / IMIDAZOLE / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.32 Å
AuthorsMarzullo, P. / Boiarska, Z. / Perez-Pena, H. / Abel, A.-C. / Alvarez-Bernad, B. / Lucena-Agell, D. / Vasile, F. / Sironi, M. / Steinmetz, M.O. / Prota, A.E. ...Marzullo, P. / Boiarska, Z. / Perez-Pena, H. / Abel, A.-C. / Alvarez-Bernad, B. / Lucena-Agell, D. / Vasile, F. / Sironi, M. / Steinmetz, M.O. / Prota, A.E. / Diaz, J.F. / Pieraccini, S. / Passarella, D.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020-MSCA-ITN-2019860070 TUBINTRAINEuropean Union
CitationJournal: Chemistry / Year: 2022
Title: Maytansinol Derivatives: Side Reactions as a Chance for New Tubulin Binders.
Authors: Marzullo, P. / Boiarska, Z. / Perez-Pena, H. / Abel, A.C. / Alvarez-Bernad, B. / Lucena-Agell, D. / Vasile, F. / Sironi, M. / Altmann, K.H. / Prota, A.E. / Diaz, J.F. / Pieraccini, S. / Passarella, D.
History
DepositionJul 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 9, 2022Group: Data collection / Category: reflns
Item: _reflns.number_obs / _reflns.pdbx_number_measured_all / _reflns.pdbx_redundancy
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)265,37324
Polymers261,6316
Non-polymers3,74118
Water13,547752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.911, 157.908, 181.461
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 , 4 types, 6 molecules ACBDEF

#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 (cattle) / Organ: Brain / References: UniProt: P81947
#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 (cattle) / Organ: Brain / References: UniProt: Q6B856
#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
#4: Protein Tubulin-Tyrosine Ligase


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 , 10 types, 770 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.: 4 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#12: Chemical ChemComp-5JS / (1S,2R,3S,5S,6S,16E,18E,20R)-11-chloro-12,20-dimethoxy-2,5,9,16-tetramethyl-8,23-dioxo-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3,5~]hexacosa-10(26),11,13,16,18,21-hexaen-6-yl phenylacetate


Mass: 665.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H41ClN2O8 / Feature type: SUBJECT OF INVESTIGATION
#13: 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
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 752 / 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: 2.8 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 3% PEG 4K, 4% glycerol, 30 mM MgCl2, 30 mM CaCl2, 0.1 M MES/Imidazole, 5 mM L-tyrosine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.32→48.02 Å / Num. obs: 130943 / % possible obs: 100 % / Redundancy: 13.709 % / Biso Wilson estimate: 51.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.183 / Rrim(I) all: 0.19 / Χ2: 0.764 / Net I/σ(I): 12.81 / Num. measured all: 1795135 / Scaling rejects: 394
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
2.32-2.3814.2633.2070.85136594957895770.3573.326100
2.38-2.4514.2312.5871.06133000934993460.4542.684100
2.45-2.5214.1912.0741.36128015902490210.5732.152100
2.52-2.5914.0481.6861.69124453886388590.661.75100
2.59-2.6813.8911.372.1118629854785400.7361.42399.9
2.68-2.7713.7461.1122.57113868828982840.7991.15499.9
2.77-2.8813.0930.8033.5104545798679850.8870.836100
2.88-312.9750.6144.5299922770277010.9270.639100
3-3.1314.0040.4436.53103642740174010.9640.459100
3.13-3.2813.5690.3288.696435710871070.9790.341100
3.28-3.4612.8250.23111.7386030670867080.9890.24100
3.46-3.6714.2850.16716.8891455640364020.9950.173100
3.67-3.9214.1310.11822.8285128602560240.9970.123100
3.92-4.2413.9740.08828.8478532562056200.9980.091100
4.24-4.6413.6710.06536.4670884518551850.9990.068100
4.64-5.1912.8450.0637.9960603471847180.9990.063100
5.19-5.9913.1910.06934.9655060417441740.9990.072100
5.99-7.3412.8610.06337.6545952357335730.9990.066100
7.34-10.3814.0450.03660.67394952812281210.038100
10.38-48.0212.6610.02969.39204101633161210.03198.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.19.1_4122refinement
XSCALEdata scaling
PDB_EXTRACT3.28data extraction
XDSdata reduction
PHENIX1.19.1_4122phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 5LXT

5lxt


Resolution: 2.32→48.02 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 6547 5 %
Rwork0.1857 124377 -
obs0.1878 130924 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.01 Å2 / Biso mean: 67.5893 Å2 / Biso min: 29.34 Å2
Refinement stepCycle: final / Resolution: 2.32→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17327 0 243 752 18322
Biso mean--67.99 58.7 -
Num. residues----2189
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.32-2.340.39832170.36524106432399
2.34-2.370.3862140.340640704284100
2.37-2.40.37862160.328741074323100
2.4-2.430.34672180.308841404358100
2.43-2.460.34242150.297340844299100
2.46-2.50.32032170.270641194336100
2.5-2.530.32082140.271340654279100
2.53-2.570.30032160.255641184334100
2.57-2.610.2882160.246240884304100
2.61-2.650.32672170.251141314348100
2.65-2.70.31282160.25241134329100
2.7-2.750.30252180.236841404358100
2.75-2.80.27822160.232840954311100
2.8-2.860.28262170.236941234340100
2.86-2.920.29562180.244841344352100
2.92-2.990.312170.244641234340100
2.99-3.060.26442160.203941154331100
3.06-3.150.24292170.193641174334100
3.15-3.240.24482180.194841514369100
3.24-3.340.24862180.188241344352100
3.34-3.460.21262180.18141394357100
3.46-3.60.23162190.174641714390100
3.6-3.770.2282190.168341494368100
3.77-3.960.20592190.149941724391100
3.96-4.210.20082200.144741854405100
4.21-4.540.14342200.129541744394100
4.54-4.990.15272210.127442044425100
4.99-5.710.19882220.160642104432100
5.71-7.20.22672250.179842674492100
7.2-48.020.18482330.167944334666100
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)
10.9839-0.10310.09093.07881.48342.77790.00170.09270.0564-0.32260.2835-0.2851-0.5960.41460.00140.5774-0.10170.08750.5762-0.14980.518628.727786.188954.0529
21.7460.7527-0.29523.10080.83882.92270.0692-0.23090.08370.4434-0.0266-0.0105-0.06220.0301-0.00010.57690.01370.07440.4876-0.1470.53318.387885.388771.8141
30.4923-0.1742-0.0852.87342.00712.78640.0141-0.11150.01720.62540.11760.00090.26090.223500.5533-0.00110.030.5393-0.11590.527922.971877.173370.0086
40.8336-0.3432-0.44770.6827-0.41450.8969-0.20710.05260.3679-0.30620.2380.2569-0.5054-0.034100.50120.04460.05140.5049-0.04640.624516.063865.229522.0629
50.460.15240.11960.31530.15220.08080.16970.19350.9084-0.2709-0.1966-0.1597-1.029-0.0854-01.03490.11430.02570.5739-0.05530.808715.237578.66322.2599
60.8691-0.412-0.66850.93790.36921.36470.15290.38040.2844-0.6485-0.0103-0.0938-0.50240.052400.58430.00330.02040.6293-0.05550.581324.600458.922413.2617
70.8511-0.0944-0.33742.78931.36733.2059-0.0136-0.07240.12890.0662-0.07450.1604-0.155-0.0832-0.02510.31950.01170.02580.4373-0.10140.511417.595556.138428.4576
80.37670.3278-0.52071.1843-0.04081.38280.0156-0.1747-0.4928-0.0158-0.12970.56710.0436-0.73-0.00420.43530.0741-0.03340.7114-0.30610.59135.34959.236538.4852
90.9768-0.30560.3260.25070.2130.7744-0.2022-0.42020.05280.45020.01920.40980.1353-1.1253-0.01350.61430.08980.07260.8482-0.1990.66385.126960.092744.7829
100.8603-0.35510.4761.07091.02421.6813-0.0651-0.17570.0950.3344-0.15490.18480.2284-0.3949-0.00010.4575-0.04240.07820.5921-0.10130.538211.939952.504139.1299
110.2933-0.00140.10991.19530.5691.1439-0.0428-0.174-0.16910.81130.036-0.20270.73260.64130.01160.57540.0185-0.01670.5862-0.06210.54925.663138.077730.5044
121.0795-0.4088-0.02382.78910.48911.846-0.0240.22160.0789-0.33960.0489-0.0247-0.18940.147500.3772-0.08970.03680.4779-0.03170.435420.229333.1555-11.9235
131.424-0.49840.35961.23960.95222.66980.0366-0.00530.08230.0165-0.19820.27080.0911-0.4335-0.00070.3528-0.06210.03040.4687-0.05410.51952.56730.2572.6194
140.9063-0.42850.03842.07191.04151.2029-0.0318-0.04050.0328-0.0251-0.07660.08990.1287-0.183900.4048-0.06540.04610.4178-0.04790.48077.197825.70634.9555
151.17950.20780.38361.19040.20210.2965-0.1375-0.1018-0.11330.57110.3082-0.3280.7780.50970.00270.46430.0786-0.0290.4247-0.08420.525325.186611.71842.5435
162.23020.19080.21661.2114-0.72122.3688-0.16090.6840.0592-0.7230.2432-0.21490.10830.0042-00.9217-0.16240.10511.0007-0.14890.540122.23766.3121-43.8886
171.5928-0.51-0.51441.67210.60112.2696-0.18660.3446-0.2971-0.25990.10860.04010.5017-0.1638-0.0010.7626-0.11720.06150.6364-0.17830.575116.3236-5.1404-26.7982
180.76920.31280.31330.36060.38570.4146-0.1942-0.028-0.03080.7190.1928-0.43920.52030.70920.00011.1359-0.02360.01490.749-0.17770.731427.507892.781782.1889
190.323-0.2078-0.43650.06240.17710.7320.02-0.0678-0.04410.46060.4245-0.56950.6470.60.01120.55180.10170.04250.8776-0.28920.806942.773728.81325.1373
200.88870.2673-0.89080.68930.08311.0814-0.22850.4548-0.51770.13310.0389-0.09520.9898-0.431801.1435-0.13290.11710.7587-0.13530.82326.059655.061369.7893
210.29290.2073-0.10140.1868-0.16730.25240.1213-0.53450.24370.3861-0.1072-0.63170.19570.953-01.08620.1104-0.00581.13680.04250.867914.175765.096298.5606
220.19820.1003-0.0210.1741-0.03340.042-0.1261-0.56670.01480.3824-0.958-0.70090.27461.1941-0.00011.28640.0396-0.25081.76010.23351.107418.236456.9882111.4819
230.18750.11230.01760.8790.81191.0176-0.0919-0.4053-0.69740.61520.0516-0.51831.02891.30080.01041.3280.26090.09961.19940.24441.07678.384851.4993104.3859
241.53951.1178-0.95281.3118-0.02661.4199-0.4304-0.0994-0.84560.38820.1325-0.29660.9522-0.0169-0.0181.40070.12970.27390.65260.12681.0259-2.10950.138299.5332
251.645-0.3602-0.85630.32650.52641.1536-0.19110.1245-0.41280.19490.30920.13610.5994-0.305300.9988-0.04810.11370.6481-0.01170.7485-0.829959.344185.6659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 243 )A1 - 243
2X-RAY DIFFRACTION2chain 'A' and (resid 244 through 311 )A244 - 311
3X-RAY DIFFRACTION3chain 'A' and (resid 312 through 438 )A312 - 438
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 27 )B1 - 27
5X-RAY DIFFRACTION5chain 'B' and (resid 28 through 64 )B28 - 64
6X-RAY DIFFRACTION6chain 'B' and (resid 65 through 127 )B65 - 127
7X-RAY DIFFRACTION7chain 'B' and (resid 128 through 259 )B128 - 259
8X-RAY DIFFRACTION8chain 'B' and (resid 260 through 296 )B260 - 296
9X-RAY DIFFRACTION9chain 'B' and (resid 297 through 338 )B297 - 338
10X-RAY DIFFRACTION10chain 'B' and (resid 339 through 401 )B339 - 401
11X-RAY DIFFRACTION11chain 'B' and (resid 402 through 437 )B402 - 437
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 199 )C1 - 199
13X-RAY DIFFRACTION13chain 'C' and (resid 200 through 338 )C200 - 338
14X-RAY DIFFRACTION14chain 'C' and (resid 339 through 401 )C339 - 401
15X-RAY DIFFRACTION15chain 'C' and (resid 402 through 440 )C402 - 440
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 127 )D1 - 127
17X-RAY DIFFRACTION17chain 'D' and (resid 128 through 441 )D128 - 441
18X-RAY DIFFRACTION18chain 'E' and (resid 6 through 46 )E6 - 46
19X-RAY DIFFRACTION19chain 'E' and (resid 47 through 141 )E47 - 141
20X-RAY DIFFRACTION20chain 'F' and (resid 1 through 66 )F1 - 66
21X-RAY DIFFRACTION21chain 'F' and (resid 67 through 127 )F67 - 127
22X-RAY DIFFRACTION22chain 'F' and (resid 128 through 165 )F128 - 165
23X-RAY DIFFRACTION23chain 'F' and (resid 166 through 207 )F166 - 207
24X-RAY DIFFRACTION24chain 'F' and (resid 208 through 297 )F208 - 297
25X-RAY DIFFRACTION25chain 'F' and (resid 298 through 380 )F298 - 380

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