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- PDB-8b7a: Tubulin - maytansinoid - 4 complex -

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Basic information

Entry
Database: PDB / ID: 8b7a
TitleTubulin - maytansinoid - 4 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 / tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / spindle microtubule ...tubulin-tyrosine ligase / tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / nervous system development / mitotic cell cycle / growth cone / microtubule / neuron projection / protein heterodimerization activity / GTPase activity / GTP binding / Golgi apparatus / ATP binding / metal ion binding / cytoplasm / cytosol
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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / IMIDAZOLE / Chem-Q0F / 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 / FOURIER SYNTHESIS / Resolution: 2.25 Å
AuthorsBoiarska, Z. / Perez-Pena, H. / Abel, A.-C. / Marzullo, P. / Alvarez-Bernad, B. / Bonato, F. / Santini, B. / Horvath, D. / Lucena-Agell, D. / Vasile, F. ...Boiarska, Z. / Perez-Pena, H. / Abel, A.-C. / Marzullo, P. / Alvarez-Bernad, B. / Bonato, F. / Santini, B. / Horvath, D. / Lucena-Agell, D. / Vasile, F. / Sironi, M. / Diaz, F.J. / Steinmetz, M.O. / Prota, A.E. / Piaraccini, S. / Passarella, D.
Funding supportEuropean Union, Switzerland, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission860070 TubInTrainEuropean Union
Swiss National Science Foundation31003A_166608 Switzerland
CitationJournal: Chemistry / Year: 2023
Title: Maytansinol Functionalization: Towards Useful Probes for Studying Microtubule Dynamics.
Authors: Boiarska, Z. / Perez-Pena, H. / Abel, A.C. / Marzullo, P. / Alvarez-Bernad, B. / Bonato, F. / Santini, B. / Horvath, D. / Lucena-Agell, D. / Vasile, F. / Sironi, M. / Diaz, J.F. / Prota, A.E. ...Authors: Boiarska, Z. / Perez-Pena, H. / Abel, A.C. / Marzullo, P. / Alvarez-Bernad, B. / Bonato, F. / Santini, B. / Horvath, D. / Lucena-Agell, D. / Vasile, F. / Sironi, M. / Diaz, J.F. / Prota, A.E. / Pieraccini, S. / Passarella, D.
History
DepositionSep 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 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)265,32725
Polymers261,6316
Non-polymers3,69619
Water16,015889
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22910 Å2
ΔGint-177 kcal/mol
Surface area79350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.271, 158.550, 181.846
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: A0A8V0Z8P0

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Non-polymers , 9 types, 908 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.: 6 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#9: 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
#10: 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
#11: Chemical ChemComp-Q0F / [(1~{R},2~{R},3~{S},5~{S},6~{S},16~{E},18~{E},20~{R},21~{S})-11-chloranyl-12,20-dimethoxy-2,5,9,16-tetramethyl-21-oxidanyl-8,23-bis(oxidanylidene)-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1^{10,14}.0^{3,5}]hexacosa-10(26),11,13,16,18-pentaen-6-yl] pent-4-enoate


Mass: 647.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H43ClN2O9 / Feature type: SUBJECT OF INVESTIGATION
#12: 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
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 889 / 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, sitting drop / pH: 6.5
Details: 5% PEG 4K, 8% 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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000029 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: 1.000029 Å / Relative weight: 1
ReflectionResolution: 2.25→48.15 Å / Num. obs: 144473 / % possible obs: 99.93 % / Redundancy: 13.6 % / Biso Wilson estimate: 50.24 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1852 / Rpim(I) all: 0.0518 / Rrim(I) all: 0.1924 / Χ2: 0.754 / Net I/σ(I): 14.23
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
2.25-2.3112.474.3080.5613064310595104770.2014.49398.9
2.31-2.3714.0943.1830.8514557510334103290.3473.302100
2.37-2.4414.2292.441.1314353810092100880.4552.53100
2.44-2.5114.1681.9161.46137952974097370.5961.987100
2.51-2.614.051.5171.84132824945794540.6851.574100
2.6-2.6913.8691.2062.35127166917291690.7631.252100
2.69-2.7913.6630.9812.88120825884588430.8331.019100
2.79-2.912.8630.6943.93109479851485110.9050.723100
2.9-3.0313.3930.5215.37109725819381930.9470.541100
3.03-3.1813.8750.3667.75108989785778550.9740.38100
3.18-3.3513.1430.2710.1897785744174400.9850.281100
3.35-3.5613.5420.18514.9795918708370830.9930.192100
3.56-3.814.2010.13121.694763667366730.9960.136100
3.8-4.1113.9650.08930.1286750621462120.9980.093100
4.11-4.513.6940.06240.0478384572657240.9990.065100
4.5-5.0313.2330.0547.7469276523552350.9990.052100
5.03-5.8112.7060.05543.1758640461546150.9990.058100
5.81-7.1113.0780.0545.9551658395039500.9990.053100
7.11-10.0613.7580.0371.46426913103310310.031100
10.06-48.1512.7310.02285.8225851798177410.02398.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
PDB_EXTRACT3.28data extraction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LXT

5lxt


Resolution: 2.25→48.15 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.223 7224 5 %
Rwork0.1809 --
obs0.1829 144457 99.89 %
Displacement parametersBiso mean: 67.09 Å2
Refinement stepCycle: final / Resolution: 2.25→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17229 0 224 889 18342
Biso mean--69.6 64 -
Num. residues----2175
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 (%)
2.25-2.270.43282320.40824411464398
2.27-2.30.40472400.346845494789100
2.3-2.330.36772380.336845304768100
2.33-2.360.35182390.323745334772100
2.36-2.390.33092390.301645484787100
2.39-2.420.33782370.285745104747100
2.42-2.460.30562390.275145274766100
2.46-2.490.29852380.26845344772100
2.49-2.530.3032400.257145454785100
2.53-2.570.30842390.256645534792100
2.57-2.620.27942380.240845194757100
2.62-2.670.28732400.248945644804100
2.67-2.720.29892400.236445494789100
2.72-2.770.26292400.220345674807100
2.77-2.830.25572400.212645584798100
2.83-2.90.22982370.192945104747100
2.9-2.970.25262410.198145724813100
2.97-3.050.25052400.188145674807100
3.05-3.140.22172400.188445444784100
3.14-3.240.23862410.18745804821100
3.24-3.360.20222410.173545804821100
3.36-3.490.20342410.166945784819100
3.49-3.650.22352420.156946084850100
3.65-3.850.16292410.147545714812100
3.85-4.090.19162430.139746144857100
4.09-4.40.17752440.129246414885100
4.4-4.840.15262430.118346154858100
4.84-5.540.19742460.140446714917100
5.54-6.980.20642470.170747074954100
6.98-48.150.21152580.16348775135100
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)
10.962-0.6248-0.58092.50690.17181.24340.20860.11630.388-0.41570.0953-0.4255-1.14130.3235-0.26660.969-0.15710.18170.5559-0.15580.577527.837598.681555.2592
20.68680.01610.18611.7210.1891.2060.0050.14690.3242-0.72080.29660.0184-0.87430.2478-0.17780.9361-0.21460.20020.5799-0.11640.596630.564894.588348.8225
31.18090.00510.35312.31961.14442.6914-0.11810.270.1524-0.7780.5988-0.7555-0.99450.724-0.45510.7348-0.22040.20510.725-0.23050.647935.51684.549745.6938
40.6624-0.4824-0.60263.11780.21972.19830.0793-0.1340.01810.19460.2732-0.5962-0.07740.7009-0.32620.3985-0.0660.05340.5497-0.24050.50132.944577.819857.7017
52.5188-0.0558-0.14842.70070.16112.22540.3979-0.22030.1268-0.066-0.1380.25780.0809-0.5523-0.28640.4550.02250.04230.5153-0.12970.476813.500980.072760.2993
61.5303-0.0852-0.52391.8286-0.04472.0218-0.02650.29640.03020.2120.2288-0.2806-0.61120.6626-0.17480.562-0.01210.06340.468-0.15630.532825.232191.077265.428
71.40831.7278-0.50553.05540.93853.73110.1512-0.27310.1240.4162-0.05460.6064-0.3164-0.4095-0.11910.47030.01460.10060.4384-0.15850.466614.074685.029370.8133
80.73680.17590.36561.99920.38460.56540.0333-0.26920.13080.51650.06780.4724-0.2106-0.0941-0.07070.69940.03560.10570.5084-0.1310.496317.398288.412780.2378
92.04610.33130.35852.98140.68022.0470.1265-0.0036-0.06360.3393-0.03420.4294-0.14930.1634-0.11230.6435-0.0070.1090.4699-0.15930.500117.9689.386574.4679
100.64740.11890.08611.45371.27522.3542-0.0321-0.14680.01580.37820.2956-0.13350.48060.5909-0.28810.46120.0617-0.02680.4561-0.14550.544527.37961.935457.5046
112.5704-0.78-0.49944.99253.22646.9105-0.174-0.1031-0.12921.45570.1808-0.38251.16970.94940.00360.81870.2021-0.15620.572-0.13290.579132.246864.24768.6142
123.5071-1.5071-0.68862.53630.19492.83170.18470.36010.6247-0.424-0.1429-0.0269-0.985-0.26660.00430.61710.06390.00830.4547-0.02440.54116.179270.569919.1142
131.6364-0.52090.04652.91941.41653.44690.02080.0340.112-0.1322-0.023-0.0311-0.25930.15-0.03860.26240.00860.02570.3894-0.11230.402823.264354.345623.0787
141.4512-1.0132-0.77341.63510.05782.93180.0637-0.09480.1807-0.1479-0.28670.4378-0.455-0.52730.23950.40390.06580.01680.4915-0.17450.554311.289262.819731.5578
152.1443-0.71420.17582.58550.32262.8145-0.23-0.1656-0.02660.2097-0.05120.6062-0.0377-1.04220.23450.42040.07670.00950.735-0.22730.55135.241960.110941.9772
160.611-0.30530.4172.56111.56193.4575-0.0519-0.10990.02570.6105-0.00690.07790.5007-0.17870.01890.3135-0.06560.03610.4365-0.05910.419817.486247.018135.5974
171.45-0.4830.00382.82420.3691.8992-0.02460.25790.1565-0.350.0462-0.0937-0.16910.177-0.0150.2711-0.07990.03390.3745-0.03190.319420.059633.3676-11.9595
181.0386-0.4632-0.02711.83371.01152.0486-0.0393-0.03730.0390.0917-0.07070.19890.0958-0.28870.10.2404-0.07310.04060.3184-0.04580.35917.305626.43223.1828
192.8677-0.39290.43332.3671-0.52132.6462-0.12920.9929-0.0451-0.94680.2051-0.0031-0.0087-0.3503-0.0370.764-0.16660.0250.9857-0.1040.430916.9379.5785-43.9253
201.6653-0.228-0.50171.71670.27662.5712-0.23610.4668-0.3738-0.29740.1527-0.0990.586-0.06720.04980.6667-0.11050.07570.5796-0.2330.4918.4072-4.4632-28.5528
211.4698-0.3755-0.03511.90250.79411.1560.0143-0.22590.09790.51980.1867-0.28050.30860.6431-0.13461.0685-0.0898-0.00210.8285-0.19010.631527.783793.186782.2471
220.4594-0.2705-0.54031.0981.08381.74330.0358-0.0905-0.0110.40830.4927-0.66180.56990.651-0.62060.44970.09120.00340.8057-0.23990.718842.676229.0495.1606
231.82630.6654-1.47472.36730.11222.4578-0.46190.3584-0.5847-0.17850.1622-0.25031.0808-0.42640.2451.0041-0.11590.14410.6234-0.14510.70236.240355.564969.8567
242.24140.3496-0.1321.9142-1.05062.53420.014-1.0687-0.23890.8689-0.3693-0.8107-0.1011.22010.32611.01180.0895-0.15931.2690.18510.855816.075462.2518105.0876
251.25341.1933-1.45321.8939-0.25553.0493-0.4293-0.372-0.95480.54780.0774-0.45351.19080.50060.21761.31990.22420.21610.66540.23351.0281.338449.2944101.4198
262.29820.5227-1.48540.84930.43672.7361-0.3142-0.2225-0.34950.24840.2939-0.11810.59850.0865-0.02770.81880.11520.10980.43830.05030.51522.389462.920891.6302
272.38080.3644-1.23292.62940.48272.998-0.45360.2614-0.43210.56450.06030.18820.9474-0.37920.38970.8416-0.08940.07690.6185-0.02150.7223-4.782756.356482.5053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 48 )A1 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 79 )A49 - 79
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 128 )A80 - 128
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 197 )A129 - 197
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 223 )A198 - 223
6X-RAY DIFFRACTION6chain 'A' and (resid 224 through 259 )A224 - 259
7X-RAY DIFFRACTION7chain 'A' and (resid 260 through 306 )A260 - 306
8X-RAY DIFFRACTION8chain 'A' and (resid 307 through 336 )A307 - 336
9X-RAY DIFFRACTION9chain 'A' and (resid 337 through 381 )A337 - 381
10X-RAY DIFFRACTION10chain 'A' and (resid 382 through 414 )A382 - 414
11X-RAY DIFFRACTION11chain 'A' and (resid 415 through 437 )A415 - 437
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 88 )B1 - 88
13X-RAY DIFFRACTION13chain 'B' and (resid 89 through 215 )B89 - 215
14X-RAY DIFFRACTION14chain 'B' and (resid 216 through 259 )B216 - 259
15X-RAY DIFFRACTION15chain 'B' and (resid 260 through 338 )B260 - 338
16X-RAY DIFFRACTION16chain 'B' and (resid 339 through 437 )B339 - 437
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 197 )C1 - 197
18X-RAY DIFFRACTION18chain 'C' and (resid 198 through 439 )C198 - 439
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 88 )D1 - 88
20X-RAY DIFFRACTION20chain 'D' and (resid 89 through 440 )D89 - 440
21X-RAY DIFFRACTION21chain 'E' and (resid 6 through 46 )E6 - 46
22X-RAY DIFFRACTION22chain 'E' and (resid 47 through 141 )E47 - 141
23X-RAY DIFFRACTION23chain 'F' and (resid 1 through 66 )F1 - 66
24X-RAY DIFFRACTION24chain 'F' and (resid 67 through 165 )F67 - 165
25X-RAY DIFFRACTION25chain 'F' and (resid 166 through 283 )F166 - 283
26X-RAY DIFFRACTION26chain 'F' and (resid 284 through 339 )F284 - 339
27X-RAY DIFFRACTION27chain 'F' and (resid 340 through 382 )F340 - 382

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