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- PDB-8cgz: tubulin-AB8939 complex -

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Basic information

Entry
Database: PDB / ID: 8cgz
Titletubulin-AB8939 complex
Components
  • Stathmin-4
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsCELL CYCLE / MICROTUBULE DYNAMICS / INHIBITOR / CYTOSKELETON / CELL DIVISION
Function / homology
Function and homology information


axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior ...axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior / microtubule depolymerization / response to L-glutamate / smoothened signaling pathway / regulation of synapse organization / startle response / locomotory exploration behavior / microtubule polymerization / regulation of microtubule polymerization or depolymerization / response to tumor necrosis factor / response to mechanical stimulus / condensed chromosome / homeostasis of number of cells within a tissue / cellular response to calcium ion / tubulin binding / adult locomotory behavior / intracellular protein transport / neuron migration / synapse organization / visual learning / neuromuscular junction / recycling endosome / cerebral cortex development / structural constituent of cytoskeleton / memory / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / neuron projection development / mitotic cell cycle / gene expression / growth cone / neuron apoptotic process / microtubule / hydrolase activity / neuron projection / protein heterodimerization activity / GTPase activity / GTP binding / protein-containing complex binding / Golgi apparatus / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / : / Tubulin beta chain / Tubulin alpha chain / Stathmin-4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Ovis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.527 Å
AuthorsVarela, P.F. / Gigant, B.
Funding support France, 1items
OrganizationGrant numberCountry
Fondation ARCARCPJA2021050003651 France
CitationJournal: TO BE PUBLISHED
Title: Development of AB8939, a Novel Colchicine-like Microtubule Synthetic Destabilizer with the Ability to Overcome Multidrug Resistance
Authors: Humbert, M. / Letard, S. / Neves, M. / Siavoshian Jeay, S. / Goubard, A. / Casteran, N. / Rebuffet, E. / Hajem, B. / Gros, L. / Varela, P.F. / Gigant, B. / Verdier, P. / Castellano, R. / ...Authors: Humbert, M. / Letard, S. / Neves, M. / Siavoshian Jeay, S. / Goubard, A. / Casteran, N. / Rebuffet, E. / Hajem, B. / Gros, L. / Varela, P.F. / Gigant, B. / Verdier, P. / Castellano, R. / Colette, Y. / Vey, N. / Pez, D. / Benjahad, A. / Moussy, A. / Mansfield, C. / Dubreuil, P.
History
DepositionFeb 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: 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 chain
B: Tubulin beta chain
C: Tubulin alpha chain
D: Tubulin beta chain
E: Stathmin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,20916
Polymers217,1555
Non-polymers3,05411
Water99155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18110 Å2
ΔGint-138 kcal/mol
Surface area65640 Å2
Unit cell
Length a, b, c (Å)65.692, 128.76, 253.204
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 5 molecules ACBDE

#1: Protein Tubulin alpha chain


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: D0VWZ0
#2: Protein Tubulin beta chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: D0VWY9
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16745.975 Da / Num. of mol.: 1 / Mutation: C14A, F20W
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

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Non-polymers , 6 types, 66 molecules

#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: 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
#7: Chemical ChemComp-UIY / 1-[4-[2-[[5-(ethoxymethyl)-2-methyl-phenyl]amino]-1,3-oxazol-5-yl]phenyl]imidazolidin-2-one


Mass: 392.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H24N4O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG, LiSO4, PIPES BUFFER, pH 6.80

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.53→126.6 Å / Num. obs: 47709 / % possible obs: 66.5 % / Redundancy: 13.1 % / CC1/2: 0.996 / Rpim(I) all: 0.04 / Rrim(I) all: 0.145 / Net I/σ(I): 12.7
Reflection shellResolution: 2.53→2.76 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1871 / CC1/2: 0.354 / Rpim(I) all: 0.521

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
autoPROCdata scaling
STARANISOdata scaling
Cootmodel building
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.527→126.6 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.368
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2444 -RANDOM
Rwork0.1972 ---
obs0.1992 47709 65.4 %-
Displacement parametersBiso mean: 94.05 Å2
Baniso -1Baniso -2Baniso -3
1-1.7865 Å20 Å20 Å2
2--1.5402 Å20 Å2
3----3.3267 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.527→126.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14295 0 195 55 14545
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00814802HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.920089HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5108SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2642HARMONIC5
X-RAY DIFFRACTIONt_it14802HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1932SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact11208SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion17.91
LS refinement shellResolution: 2.53→2.73 Å
RfactorNum. reflection% reflection
Rfree0.3122 50 -
Rwork0.2874 --
obs0.2887 955 6.57 %
Refinement TLS params.

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)
12.47570.0081-0.96065.1658-1.62974.2979-0.22660.3430.31750.3430.2338-0.09120.3175-0.0912-0.00720.15440.11790.124-0.10590.1852-0.1386-9.1745-31.89351.6109
21.76421.37410.26044.2658-0.27462.1659-0.01750.2433-0.15310.2433-0.0133-0.2045-0.1531-0.20450.03080.14580.0070.0327-0.03960.0273-0.1936-1.97347.492534.9196
31.81281.3844-0.55883.9436-1.05111.65420.19240.6522-0.0240.6522-0.1244-0.0914-0.024-0.0914-0.0680.1128-0.10140.1848-0.04480.0083-0.042712.955845.948722.5705
42.85621.0938-0.3043.2407-0.33482.1610.24570.4856-0.22550.4856-0.2864-0.0053-0.2255-0.00530.0407-0.037-0.04510.025-0.00350.0247-0.039934.037380.62299.3872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|613 E|4 - E|64 }A1 - 437
2X-RAY DIFFRACTION1{ A|1 - A|613 E|4 - E|64 }A600 - 601
3X-RAY DIFFRACTION1{ A|1 - A|613 E|4 - E|64 }A610 - 613
4X-RAY DIFFRACTION1{ A|1 - A|613 E|4 - E|64 }E7 - 64
5X-RAY DIFFRACTION2{ B|1 - B|4000 E|65 - E|89 }B1 - 440
6X-RAY DIFFRACTION2{ B|1 - B|4000 E|65 - E|89 }B501 - 600
7X-RAY DIFFRACTION2{ B|1 - B|4000 E|65 - E|89 }E65 - 89
8X-RAY DIFFRACTION3{ C|1 - C|613 E|90 - E|115 }C1 - 439
9X-RAY DIFFRACTION3{ C|1 - C|613 E|90 - E|115 }C600 - 601
10X-RAY DIFFRACTION3{ C|1 - C|613 E|90 - E|115 }C610 - 613
11X-RAY DIFFRACTION3{ C|1 - C|613 E|90 - E|115 }E90 - 115
12X-RAY DIFFRACTION4{ D|1 - D|4000 E|116 - E|145 }D1 - 441
13X-RAY DIFFRACTION4{ D|1 - D|4000 E|116 - E|145 }D501 - 600
14X-RAY DIFFRACTION4{ D|1 - D|4000 E|116 - E|145 }E116 - 141

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