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- PDB-8wd0: Crystal structure of T2R-TTL-Erianin complex -

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Basic information

Entry
Database: PDB / ID: 8wd0
TitleCrystal structure of T2R-TTL-Erianin complex
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta chain
  • Tubulin tyrosine ligase
KeywordsCELL CYCLE / Microtubule
Function / homology
Function and homology information


microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / tubulin binding / cellular response to interleukin-4 / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / mitotic cell cycle ...microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / tubulin binding / cellular response to interleukin-4 / structural constituent of cytoskeleton / microtubule cytoskeleton organization / 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 / GTPase activity / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / metal ion binding / cytoplasm / cytosol
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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / : / Tubulin beta chain / Stathmin-4 / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Gallus gallus (chicken)
Bos taurus (domestic cattle)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Bioorg.Chem. / Year: 2024
Title: The cytotoxic natural compound erianin binds to colchicine site of beta-tubulin and overcomes taxane resistance
Authors: Yan, W. / Zhou, Y. / Yuan, X. / Bai, P. / Tang, M. / Chen, L. / Wei, H. / Yang, J.
History
DepositionSep 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 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-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)269,97921
Polymers266,3606
Non-polymers3,61915
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.560, 181.540, 104.740
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
d_1ens_1
d_2ens_1
d_1ens_2
d_2ens_2
/ NCS ensembles :
ID
ens_2
ens_1

NCS oper:
IDCodeMatrixVector
1given(0.94850117861, 0.128412871991, 0.289578397817), (-0.181355203113, 0.969640365436, 0.164036130228), (-0.259722552889, -0.208105012009, 0.942993371927)-64.7068536318, -52.7058919498, 23.3548513503
2given(0.95352378858, 0.119815078654, 0.276471936258), (-0.173717137911, 0.968298604343, 0.17949977388), (-0.246200610493, -0.219185217919, 0.944109686233)-64.3153888204, -53.3088755302, 23.2719695912

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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 (domestic cattle) / References: UniProt: P81947
#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: 22125.301 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: 43825.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli)

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Non-polymers , 9 types, 82 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.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-W4F / 2-methoxy-5-[2-(3,4,5-trimethoxyphenyl)ethyl]phenol / Erianin


Mass: 318.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22O5 / Feature type: SUBJECT OF INVESTIGATION
#11: 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
#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.: 67 / 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: 3.02 Å3/Da / Density % sol: 59.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 6% poly(ethylene glycol) 4000, 8% glycerol, 0.1 M MES (pH 6.7), 30 mM CaCl2 and 30 mM MgCl2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.6→38.26 Å / Num. obs: 91318 / % possible obs: 99 % / Redundancy: 13.1 % / Biso Wilson estimate: 61.85 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.7
Reflection shellResolution: 2.6→2.67 Å / Num. unique obs: 1085 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→38.26 Å / SU ML: 0.3556 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1898
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2579 2000 2.19 %
Rwork0.2268 89227 -
obs0.2275 91227 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.69 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17184 0 197 67 17448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007317759
X-RAY DIFFRACTIONf_angle_d0.829724092
X-RAY DIFFRACTIONf_chiral_restr0.11632630
X-RAY DIFFRACTIONf_plane_restr0.00483116
X-RAY DIFFRACTIONf_dihedral_angle_d22.47716516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.30371410.27526320X-RAY DIFFRACTION98.79
2.67-2.740.32141410.2826262X-RAY DIFFRACTION98.74
2.74-2.820.31451410.28126323X-RAY DIFFRACTION98.76
2.82-2.910.32661420.28376313X-RAY DIFFRACTION98.59
2.91-3.010.3381410.28066305X-RAY DIFFRACTION99.14
3.01-3.130.30481430.25986345X-RAY DIFFRACTION99.14
3.13-3.280.30151410.26156352X-RAY DIFFRACTION98.74
3.28-3.450.28161430.25516340X-RAY DIFFRACTION99.39
3.45-3.660.27751410.24536310X-RAY DIFFRACTION98.2
3.66-3.950.26711420.22576343X-RAY DIFFRACTION98.3
3.95-4.340.23491450.20566424X-RAY DIFFRACTION99.18
4.34-4.970.20831440.17966454X-RAY DIFFRACTION99.29
4.97-6.260.231460.22056504X-RAY DIFFRACTION99.24
6.26-38.260.23841490.20656632X-RAY DIFFRACTION97.79

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