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- PDB-7dad: EPD in complex with tubulin -

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Basic information

Entry
Database: PDB / ID: 7dad
TitleEPD in complex with tubulin
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta chain
  • Tubulin tyrosine ligase
KeywordsCELL CYCLE / EPD / tubulin / protein-drug complex
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins ...tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / microtubule depolymerization / COPI-mediated anterograde transport / 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 / mitotic cell cycle / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / GTPase activity / nucleotide binding / GTP binding / Golgi apparatus / metal ion binding / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / EPOTHILONE D / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsWang, Y. / Wu, C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: High-resolution X-ray structure of three microtubule-stabilizing agents in complex with tubulin provide a rationale for drug design.
Authors: Xiao, Q. / Xue, T. / Shuai, W. / Wu, C. / Zhang, Z. / Zhang, T. / Zeng, S. / Sun, B. / Wang, Y.
History
DepositionOct 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 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 chain
C: Tubulin alpha-1B chain
D: Tubulin beta chain
E: Stathmin-4
F: Tubulin tyrosine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,34924
Polymers261,6316
Non-polymers3,71718
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23880 Å2
ΔGint-142 kcal/mol
Surface area81510 Å2
Unit cell
Length a, b, c (Å)105.163, 158.506, 181.605
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) Sus scrofa (pig) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AGU7
#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.) Mus musculus (house mouse) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63042
#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 , 8 types, 18 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-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
#10: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Chemical ChemComp-EPD / EPOTHILONE D


Mass: 491.683 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H41NO5S / 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

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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: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 6% PEG, 5% glycerol, 0.1 M MES, 30 mM CaCl2, 30 mM MgCL2, pH 6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.849→50 Å / Num. obs: 71614 / % possible obs: 100 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.058 / Rrim(I) all: 0.214 / Χ2: 0.986 / Net I/σ(I): 3.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.85-2.912.91.00935230.8170.2881.050.936100
2.9-2.9513.60.94135440.830.2620.9780.938100
2.95-3.0113.90.81235400.8840.2240.8430.961100
3.01-3.0713.80.71235290.9040.1970.7390.956100
3.07-3.1413.70.61535300.9310.1710.6390.981100
3.14-3.2113.60.55135430.9410.1540.5720.982100
3.21-3.2913.40.46435590.9540.1310.4830.997100
3.29-3.3812.80.4235320.960.1220.4381.005100
3.38-3.4812.80.35835500.970.1030.3731.01999.9
3.48-3.5913.30.31935540.9780.090.3321.03100
3.59-3.7213.90.30235570.9780.0830.3131.029100
3.72-3.8713.80.23235740.9880.0640.2411.029100
3.87-4.0413.70.18835880.9910.0520.1961.039100
4.04-4.2613.50.15635370.9940.0440.1631.021100
4.26-4.5212.60.13435890.9940.0390.1391.021100
4.52-4.8713.40.1236010.9940.0340.1251.016100
4.87-5.3613.90.12936090.9940.0360.1340.998100
5.36-6.1413.40.13436330.9940.0380.1390.955100
6.14-7.7312.60.10936700.9950.0320.1140.919100
7.73-5012.30.07338520.9970.0210.0760.883100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I55

4i55


Resolution: 2.85→49.907 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2257 2000 2.82 %
Rwork0.1786 68925 -
obs0.1799 70925 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.68 Å2 / Biso mean: 49.6376 Å2 / Biso min: 5.92 Å2
Refinement stepCycle: final / Resolution: 2.85→49.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17488 0 223 0 17711
Biso mean--56.28 --
Num. residues----2209
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.85-2.92030.38011330.2849456593
2.9203-2.99930.3161390.2403483799
2.9993-3.08750.30891430.21964927100
3.0875-3.18720.31471420.21274895100
3.1872-3.30110.27291440.22394932100
3.3011-3.43320.27181420.20154897100
3.4332-3.58940.25051440.19034950100
3.5894-3.77860.25941420.17874926100
3.7786-4.01520.20991440.15954953100
4.0152-4.32510.18491450.14524981100
4.3251-4.760.16861440.12744969100
4.76-5.44810.18421460.14485005100
5.4481-6.86120.19481440.1895501299
6.8612-49.9070.19511480.1826507696

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