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- PDB-8diq: Tubulin-RB3_SLD-TTL in complex with SB226 -

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Basic information

Entry
Database: PDB / ID: 8diq
TitleTubulin-RB3_SLD-TTL in complex with SB226
Components
  • Stathmin-4
  • Tubulin Tyrosine Ligase
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE/INHIBITOR / MICROTUBULE INHIBITOR / COLCHICINE / CELL CYCLE / CANCER / CELL CYCLE-INHIBITOR 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 / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-JVI / Tubulin beta chain / Tubulin tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Gallus gallus (chicken)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.395 Å
AuthorsWhite, S.W. / Yun, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA148706 United States
CitationJournal: Cancer Lett. / Year: 2022
Title: SB226, an inhibitor of tubulin polymerization, inhibits paclitaxel-resistant melanoma growth and spontaneous metastasis.
Authors: Deng, S. / Banerjee, S. / Chen, H. / Pochampally, S. / Wang, Y. / Yun, M.K. / White, S.W. / Parmar, K. / Meibohm, B. / Hartman, K.L. / Wu, Z. / Miller, D.D. / Li, W.
History
DepositionJun 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)265,34225
Polymers261,3056
Non-polymers4,03719
Water6,269348
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.491, 158.414, 181.226
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 50041.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta-2B 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.) 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, 367 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#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-JVI / 4-[2-(ethylamino)-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl]-7-methoxy-3,4-dihydroquinoxalin-2(1H)-one


Mass: 339.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H21N5O2 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 348 / 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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG4K, MES, Glycerol, CaCl2, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.39→19.92 Å / Num. obs: 119484 / % possible obs: 99.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 48.06 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.055 / Net I/σ(I): 12.7
Reflection shellResolution: 2.39→2.44 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.919 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5742 / CC1/2: 0.691 / Rpim(I) all: 0.594 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6BR1

6br1


Resolution: 2.395→19.92 Å / SU ML: 0.2496 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.4002 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2095 2000 1.68 %
Rwork0.1817 117387 -
obs0.1822 119387 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.98 Å2
Refinement stepCycle: LAST / Resolution: 2.395→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17068 0 250 348 17666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002217691
X-RAY DIFFRACTIONf_angle_d0.504723987
X-RAY DIFFRACTIONf_chiral_restr0.0412609
X-RAY DIFFRACTIONf_plane_restr0.00373098
X-RAY DIFFRACTIONf_dihedral_angle_d17.785510558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.450.31761390.26548155X-RAY DIFFRACTION98.24
2.45-2.520.26531420.24518307X-RAY DIFFRACTION100
2.52-2.60.24021410.2328303X-RAY DIFFRACTION99.98
2.6-2.680.25721420.21958330X-RAY DIFFRACTION99.99
2.68-2.770.23891420.22468327X-RAY DIFFRACTION100
2.77-2.880.261410.21928325X-RAY DIFFRACTION99.99
2.88-3.020.24421430.21478373X-RAY DIFFRACTION100
3.02-3.170.24961430.20858362X-RAY DIFFRACTION100
3.17-3.370.24671420.20558359X-RAY DIFFRACTION100
3.37-3.630.21031420.18348381X-RAY DIFFRACTION99.99
3.63-3.990.18831440.16118403X-RAY DIFFRACTION100
3.99-4.570.15331440.14288471X-RAY DIFFRACTION100
4.57-5.730.1771460.1538520X-RAY DIFFRACTION100
5.73-19.920.20161490.16918771X-RAY DIFFRACTION99.87
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)
10.742344189271-0.1680144826840.1483432161893.075378931531.256295732822.56712124540.0214620860878-0.047070093731-0.0477193679996-0.02552162426770.169827052736-0.1403827203150.305969614410.242999468472-0.171266027920.3451363285730.0389221550115-0.04219005157210.368697100274-0.1076756923050.37583629483925.6383398754-83.4959618821-61.5250911961
21.123838879210.5371190259650.3633303358891.808277801421.257763583672.587070599150.06169776283610.000980182269947-0.1675454769880.0442968163027-0.0652986138060.1038056178320.273977334129-0.123284448851-0.01188679021010.2690102586080.00646519358864-0.01850510033480.361449939724-0.0923759907020.40379584470115.8432916805-57.6751343474-29.4447826248
30.805567426365-0.02008252465210.001136423455121.177352660020.5330217626711.50157336019-0.0477579952644-0.12063355041-0.1017927575750.09987048969330.02573713906010.1018840861370.0530016359039-0.07185729484720.02103430465570.2267360594830.03800799006320.007467084601080.290403089822-0.01289392584840.30841389665413.0735076605-29.39920507313.66472021752
42.06118078235-0.3811777793080.3741049771311.996941072460.01004825988072.19108949315-0.310700554733-0.7392536889370.1926963321240.602233055580.32320762903-0.090575160015-0.341735820207-0.098144047915-0.02460190781380.6534584293130.168055835777-0.040743307750.648398483323-0.188073163380.39966270942918.27879778071.4066067611131.953429788
50.2283118283450.2663467114580.3636347898662.07794749632.197443014442.73577015884-0.05071171823710.0498839769583-0.0224865223389-0.3729401463080.572066108308-0.545161928296-0.4191288157170.727804193802-0.6284856483140.456564398086-0.0126560807191-0.04045971579770.699529452818-0.1857982602690.63424462077139.705951242-42.5216745607-21.5665040352
62.84496811232-0.3216738275242.11997873341.95436224737-0.6438209778283.22947882697-0.5021023700380.2947035132510.807621234367-0.1592148387140.0840369898437-0.262229506629-0.8861837465880.2538048772960.2550829251770.77151911375-0.0940872534999-0.1266329690530.4064685746140.08482279302340.6601297765114.13426106261-56.3479421609-91.2900253872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 437)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 503)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 440)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 501)
5X-RAY DIFFRACTION5(chain 'E' and resid 6 through 140)
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 380)

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