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- PDB-7e4z: Crystal structure of tubulin in complex with Maytansinol -

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Basic information

Entry
Database: PDB / ID: 7e4z
TitleCrystal structure of tubulin in complex with Maytansinol
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin tyrosine ligase
KeywordsSTRUCTURAL PROTEIN/INHIBITOR / microtubule assembly inhibitors / STRUCTURAL PROTEIN-INHIBITOR complex
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 / cytoplasm / cytosol
Similarity search - Function
Rossmann fold - #11480 / 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. ...Rossmann fold - #11480 / 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. / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Chem-BKL / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Rattus norvegicus (Norway rat)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsWang, Y. / Li, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81703553 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: C3 ester side chain plays a pivotal role in the antitumor activity of Maytansinoids.
Authors: Li, W. / Huang, M. / Li, Y. / Xia, A. / Tan, L. / Zhang, Z. / Wang, Y. / Yang, J.
History
DepositionFeb 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)259,36225
Polymers255,3766
Non-polymers3,98619
Water6,738374
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Hetero 6-mer - A2B2C1D1
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23520 Å2
ΔGint-142 kcal/mol
Surface area81000 Å2
Unit cell
Length a, b, c (Å)104.431, 156.635, 182.275
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: 48966.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 48391.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: TUBB2B / Production host: Escherichia coli (E. coli) / References: UniProt: Q6B856
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16282.527 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 , 9 types, 393 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 3 / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#11: Chemical ChemComp-BKL / (1R,2S,3S,5S,6S,16E,18E,20R,21S)-11-chloro-6,21-dihydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3,5~]hexacosa-10(26),11,13,16,18-pentaene-8,23-dione


Mass: 565.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H37ClN2O8 / 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.: 374 / 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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 6% poly(ethylene glycol) 4000, 8% glycerol, 0.1 M MES (pH 6.7), 30 mM CaCl2, 30 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97908 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.69→40 Å / Num. obs: 83413 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 45.03 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.037 / Rrim(I) all: 0.138 / Χ2: 0.616 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.7-2.813.90.72382120.9390.1990.750.462
2.8-2.9113.70.5482770.9620.150.560.47
2.91-3.0413.40.40782410.9760.1150.4230.488
3.04-3.212.60.29182480.9840.0850.3040.533
3.2-3.413.80.21382790.9910.0590.2210.585
3.4-3.6613.80.15482840.9950.0430.160.672
3.66-4.0313.30.11683550.9960.0330.1210.785
4.03-4.6213.30.08983500.9970.0250.0930.836
4.62-5.8113.50.07984380.9980.0220.0820.717
5.81-4012.50.05787290.9980.0170.060.606

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TV8

4tv8


Resolution: 2.69→38.285 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 4059 4.88 %
Rwork0.1923 79133 -
obs0.194 83192 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 209.23 Å2 / Biso mean: 49.62 Å2 / Biso min: 12.29 Å2
Refinement stepCycle: final / Resolution: 2.69→38.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17406 0 370 374 18150
Biso mean--62.15 37.68 -
Num. residues----2197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00218222
X-RAY DIFFRACTIONf_angle_d0.64624760
X-RAY DIFFRACTIONf_chiral_restr0.0282695
X-RAY DIFFRACTIONf_plane_restr0.0023208
X-RAY DIFFRACTIONf_dihedral_angle_d14.4476809
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.69-2.72150.33991280.2612245091
2.7215-2.75470.29551500.25862705100
2.7547-2.78950.31511530.26322668100
2.7895-2.82620.25241440.2412711100
2.8262-2.86490.29951400.2442695100
2.8649-2.90590.2911460.2352728100
2.9059-2.94920.2471470.25112692100
2.9492-2.99530.26031500.23312710100
2.9953-3.04440.27681310.23292742100
3.0444-3.09680.24451440.24112688100
3.0968-3.15310.27661360.23342744100
3.1531-3.21380.2771370.23462701100
3.2138-3.27930.27351370.22292737100
3.2793-3.35060.27491260.22082731100
3.3506-3.42850.27561360.21082729100
3.4285-3.51420.26181440.2042716100
3.5142-3.60910.24591320.19292736100
3.6091-3.71520.25381310.18432736100
3.7152-3.8350.20531430.17532740100
3.835-3.9720.2251390.1732740100
3.972-4.13080.20491580.16762736100
4.1308-4.31860.20881270.16472748100
4.3186-4.54590.19061420.14952770100
4.5459-4.83020.16651260.14692767100
4.8302-5.20230.20411300.15962783100
5.2023-5.72430.22621540.17762774100
5.7243-6.5490.19681240.19092820100
6.549-8.23760.21111570.17892817100
8.2376-38.2850.15371470.1537281996

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