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- PDB-7lz8: Tubulin-RB3_SLD-TTL in complex with compound 5t -

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Basic information

Entry
Database: PDB / ID: 7lz8
TitleTubulin-RB3_SLD-TTL in complex with compound 5t
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-YJ4 / 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: 2.92 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: J.Med.Chem. / Year: 2021
Title: X-ray Crystallography-Guided Design, Antitumor Efficacy, and QSAR Analysis of Metabolically Stable Cyclopenta-Pyrimidinyl Dihydroquinoxalinone as a Potent Tubulin Polymerization Inhibitor.
Authors: Banerjee, S. / Mahmud, F. / Deng, S. / Ma, L. / Yun, M.K. / Fakayode, S.O. / Arnst, K.E. / Yang, L. / Chen, H. / Wu, Z. / Lukka, P.B. / Parmar, K. / Meibohm, B. / White, S.W. / Wang, Y. / Li, W. / Miller, D.D.
History
DepositionMar 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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)265,24325
Polymers261,3056
Non-polymers3,93819
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.570, 155.041, 182.339
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 , 9 types, 56 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.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / 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-YJ4 / 4-[2-(ethylamino)pyrido[3,2-d]pyrimidin-4-yl]-7-methoxy-3,4-dihydroquinoxalin-2(1H)-one


Mass: 350.375 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18N6O2 / 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.: 37 / 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: 56.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: PEG 4000, MES, glycerol, CaCl2, MgCl2, ethyl acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 64109 / % possible obs: 98.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 78.5 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.048 / Net I/σ(I): 16.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.869 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6296 / CC1/2: 0.465 / Rpim(I) all: 0.506 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6BR1

6br1


Resolution: 2.92→45.36 Å / SU ML: 0.3362 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.4841 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2276 2000 3.12 %
Rwork0.1844 62032 -
obs0.1858 64032 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.59 Å2
Refinement stepCycle: LAST / Resolution: 2.92→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16533 0 227 37 16797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002817122
X-RAY DIFFRACTIONf_angle_d0.617323212
X-RAY DIFFRACTIONf_chiral_restr0.04312530
X-RAY DIFFRACTIONf_plane_restr0.00452998
X-RAY DIFFRACTIONf_dihedral_angle_d17.283110222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.92-2.990.31951300.294046X-RAY DIFFRACTION90.76
2.99-3.070.33581420.26874375X-RAY DIFFRACTION98.28
3.07-3.160.3111380.25194293X-RAY DIFFRACTION96.26
3.16-3.260.28291430.22714433X-RAY DIFFRACTION99.26
3.26-3.380.24151440.21094480X-RAY DIFFRACTION99.83
3.38-3.510.2781430.19164451X-RAY DIFFRACTION99.83
3.51-3.670.23431450.17724463X-RAY DIFFRACTION99.46
3.67-3.870.21811440.17454479X-RAY DIFFRACTION99.48
3.87-4.110.18451430.16724447X-RAY DIFFRACTION99.44
4.11-4.430.22671440.15684467X-RAY DIFFRACTION98.61
4.43-4.870.19691410.14774374X-RAY DIFFRACTION96.6
4.87-5.580.2041470.1754547X-RAY DIFFRACTION99.79
5.58-7.020.24931470.20214582X-RAY DIFFRACTION99.45
7.02-45.360.20351490.17934595X-RAY DIFFRACTION96.19
Refinement TLS params.Method: refined / Origin x: 17.4993427456 Å / Origin y: -42.736401387 Å / Origin z: -23.7185054805 Å
111213212223313233
T0.48440388769 Å2-0.0314100450331 Å2-0.0133764249505 Å2-0.605875581276 Å2-0.0408036295961 Å2--0.66131595425 Å2
L0.260788486852 °20.0453865223955 °20.193459544448 °2-0.781472454931 °20.710421241719 °2--1.29097169238 °2
S-0.0410949742283 Å °-0.023226536028 Å °-0.0415377958782 Å °-0.016791217304 Å °0.127407787126 Å °-0.00808114142837 Å °-0.00781681218539 Å °0.0588740345821 Å °-0.000105590592659 Å °
Refinement TLS groupSelection details: all

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