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- PDB-5sbb: Tubulin-maytansinoid-4c-complex -

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Basic information

Entry
Database: PDB / ID: 5sbb
TitleTubulin-maytansinoid-4c-complex
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin-Tyrosine LigaseTubulin—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 / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / spindle microtubule / protein modification process / structural constituent of cytoskeleton ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / mitotic cell cycle / nervous system development / growth cone / microtubule / neuron projection / protein heterodimerization activity / nucleotide binding / GTPase activity / 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. / 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
Chem-5JH / 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: 2.25 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)265,38524
Polymers261,6316
Non-polymers3,75318
Water15,619867
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.615, 157.484, 180.633
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 / 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, 885 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine 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 / Guanosine 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 / MES (buffer)


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 / Glycerol


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


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#12: Chemical ChemComp-5JH / (1R,2R,3S,5S,6S,16E,18E,20R,21S)-11-chloro-21-hydroxy-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-pentaen-6-yl heptanoate


Mass: 677.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H49ClN2O9 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 867 / 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: 2.25→49.54 Å / Num. obs: 141155 / % possible obs: 99.3 % / Redundancy: 13.728 % / Biso Wilson estimate: 44.41 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.189 / Rrim(I) all: 0.196 / Χ2: 0.768 / Net I/σ(I): 11.75 / Num. measured all: 1937774 / Scaling rejects: 202
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
2.25-2.3113.0772.4890.9913368710374102230.4082.59198.5
2.31-2.3714.3461.9471.391431611012399790.5482.01898.6
2.37-2.4414.4041.6551.67139937983197150.631.71598.8
2.44-2.5214.3191.3122.12135903957694910.7531.3699.1
2.52-2.614.1741.0612.62130030925791740.811.199.1
2.6-2.6914.0110.8983.1124490899088850.850.93298.8
2.69-2.7913.7870.7163.89118964867986290.90.74399.4
2.79-2.912.9080.5434.94107249838683090.9330.56599.1
2.9-3.0313.5710.4126.63108178800979710.9610.42899.5
3.03-3.1813.9520.318.97106301767176190.980.32299.3
3.18-3.3513.1730.23311.2996256732973070.9880.24299.7
3.35-3.5613.7210.16615.8194152689568620.9930.17299.5
3.56-3.814.2990.12121.5593287654865240.9970.12699.6
3.8-4.1114.0870.09226.8285647609660800.9980.09599.7
4.11-4.513.8230.07331.9477660563156180.9990.07699.8
4.5-5.0313.2370.06435.0967511510851000.9980.06699.8
5.03-5.8112.7960.0731.658147454845440.9980.07399.9
5.81-7.1213.1040.0731.9850305384138390.9980.07399.9
7.12-10.0613.7770.04945.242005304930490.9990.051100
10.06-49.5412.7580.04250.4422173176117380.9990.04498.7

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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: 2.25→49.54 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 7056 5 %
Rwork0.1833 134076 -
obs0.1854 141132 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.27 Å2 / Biso mean: 58.6411 Å2 / Biso min: 26.16 Å2
Refinement stepCycle: final / Resolution: 2.25→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17316 0 243 867 18426
Biso mean--58.52 53.77 -
Num. residues----2187
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 (%)
2.25-2.270.34282290.32694356458597
2.27-2.30.32842310.29643874618100
2.3-2.330.31632310.28524397462898
2.33-2.360.29262340.279344324666100
2.36-2.390.32952300.27284386461698
2.39-2.420.33482340.26734434466899
2.42-2.460.29112320.25614409464199
2.46-2.490.30232310.24264397462898
2.49-2.530.27362320.233444064638100
2.53-2.570.28192320.23054410464299
2.57-2.620.28742340.22194434466899
2.62-2.660.26112360.222944854721100
2.66-2.720.27092310.20884382461399
2.72-2.770.23852330.21234435466899
2.77-2.830.27272340.22284442467699
2.83-2.90.26472350.226944724707100
2.9-2.970.27532350.21334453468899
2.97-3.050.23652340.19384448468299
3.05-3.140.23952340.18674453468799
3.14-3.240.24342360.18944475471199
3.24-3.360.23412370.182345054742100
3.36-3.490.21222360.17574490472699
3.49-3.650.20572350.168344714706100
3.65-3.840.19192390.152645304769100
3.84-4.080.17892360.146844944730100
4.08-4.40.18682390.137445384777100
4.4-4.840.17472400.129845554795100
4.84-5.540.20322410.156645754816100
5.54-6.980.22322440.183246364880100
6.98-49.540.21362510.170647895040100
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)
10.0374-0.1654-0.2317-0.03370.06630.3738-0.0164-0.0616-0.02450.33050.5674-0.62230.44670.77220.02120.46750.06180.0440.8068-0.29960.735142.835729.225.4605
20.94360.245-0.93770.72140.20051.1902-0.25230.4089-0.5204-0.1314-0.0394-0.18610.8305-0.337400.9819-0.13730.16280.636-0.14630.68036.118754.688969.8745
30.28660.09460.1350.0793-0.00350.13450.2541-0.41250.11630.1833-0.1144-0.5539-0.45250.7790.00010.7603-0.0295-0.03520.88620.03980.689711.146265.762997.455
4-00.0001-0.00210.1379-0.03050.0060.0595-0.09660.25480.0564-0.5016-1.15990.12370.5127-0.00171.0377-0.1053-0.29541.73810.37161.11821.619962.0724109.889
50.09210.12570.05820.15520.07760.03370.2095-0.35910.13360.96690.1617-1.17270.27561.05860.00061.08130.1865-0.09821.72460.44561.214318.801753.2978108.5343
61.26950.5431-0.94720.79810.20411.2777-0.4837-0.26-0.88750.1896-0.063-0.30991.13590.1554-0.12811.20130.10760.26980.55270.2150.9621-1.793947.587101.1246
71.8186-0.2219-1.50730.53670.15771.2476-0.17520.1069-0.2914-0.0110.15440.14740.2794-0.202800.7406-0.02160.0880.5034-0.00940.6226-0.944460.225687.2986
80.91440.0211-0.14452.97711.39212.38960.00460.05270.0728-0.23390.2198-0.2133-0.48040.29360.00250.4619-0.07030.06840.4461-0.10960.430528.696385.814455.9782
90.86730.5383-0.07690.93060.54520.9890.2034-0.2511-0.03830.4324-0.30570.73790.0168-0.5264-00.57460.00070.14530.5331-0.17150.59959.153884.455171.7016
100.62560.1360.17562.52821.6331.93760.0138-0.09640.0040.60190.03030.08410.25670.075900.5466-0.00210.05230.446-0.06640.425522.962476.865869.9824
111.6167-0.5056-0.13971.162-0.54080.98180.12690.26270.4535-0.2017-0.07880.1337-0.6871-0.1918-00.6020.05110.01540.4987-0.02330.596516.32469.981619.4157
121.0806-0.62-0.04571.66281.36133.0326-0.03390.00370.06960.059-0.15870.1449-0.1588-0.3422-0.04760.31590.00270.02210.4358-0.11430.456715.606756.997930.6786
130.08520.09890.37441.15251.06621.9951-0.0235-0.06770.00280.5062-0.10.09690.3975-0.1306-0.00050.4029-0.05440.07470.4535-0.0670.457417.702646.279835.6346
143.53-3.0979-4.88995.93956.30068.0269-0.0681-0.01170.0083-0.12680.0426-0.0320.01160.0665-0.01131.4446-0.2473-0.3670.8132-0.02630.842618.783346.148656.7722
150.89-0.17650.16572.90980.14511.607-0.05840.1220.0826-0.28030.0897-0.0121-0.14020.16900.3228-0.06710.03610.4125-0.03530.387720.349533.0378-11.912
160.8314-0.372-0.10881.68361.1871.7009-0.0277-0.01770.07360.0942-0.06420.12780.0888-0.1859-0.00150.2794-0.06610.04920.3713-0.02610.3937.632625.89533.2025
171.7397-0.03371.02690.9554-0.3180.9369-0.17090.46450.2428-0.69040.2031-0.0796-0.0648-0.07740.00020.7831-0.10710.04780.7704-0.06960.471917.40359.7621-43.9124
181.2542-0.4809-0.27711.35790.11312.1082-0.17840.3206-0.1403-0.46640.1363-0.26060.31160.2136-00.6634-0.00970.11260.6486-0.19420.498625.719-4.2727-36.5949
191.3513-0.3252-0.3661.49640.70331.7992-0.11690.1724-0.2474-0.10180.06810.08460.3748-0.115800.5688-0.07230.04180.4812-0.11170.476613.8009-4.7236-23.969
200.76070.33440.28470.36330.39670.414-0.17410.0391-0.04930.91460.0842-0.24430.44340.5357-0.00011.1101-0.02450.03960.6903-0.11620.626827.446892.567981.9993
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E' and (resid 47 through 140 )E47 - 140
2X-RAY DIFFRACTION2chain 'F' and (resid 1 through 66 )F1 - 66
3X-RAY DIFFRACTION3chain 'F' and (resid 67 through 96 )F67 - 96
4X-RAY DIFFRACTION4chain 'F' and (resid 97 through 140 )F97 - 140
5X-RAY DIFFRACTION5chain 'F' and (resid 141 through 184 )F141 - 184
6X-RAY DIFFRACTION6chain 'F' and (resid 185 through 283 )F185 - 283
7X-RAY DIFFRACTION7chain 'F' and (resid 284 through 380 )F284 - 380
8X-RAY DIFFRACTION8chain 'A' and (resid 1 through 273 )A1 - 273
9X-RAY DIFFRACTION9chain 'A' and (resid 274 through 311 )A274 - 311
10X-RAY DIFFRACTION10chain 'A' and (resid 312 through 438 )A312 - 438
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 88 )B1 - 88
12X-RAY DIFFRACTION12chain 'B' and (resid 89 through 338 )B89 - 338
13X-RAY DIFFRACTION13chain 'B' and (resid 339 through 437 )B339 - 437
14X-RAY DIFFRACTION14chain 'B' and (resid 438 through 439 )B438 - 439
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 199 )C1 - 199
16X-RAY DIFFRACTION16chain 'C' and (resid 200 through 440 )C200 - 440
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 88 )D1 - 88
18X-RAY DIFFRACTION18chain 'D' and (resid 89 through 223 )D89 - 223
19X-RAY DIFFRACTION19chain 'D' and (resid 224 through 441 )D224 - 441
20X-RAY DIFFRACTION20chain 'E' and (resid 6 through 46 )E6 - 46

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  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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