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- PDB-6x1e: Tubulin-RB3_SLD-TTL in complex with compound 5l -

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Basic information

Entry
Database: PDB / ID: 6x1e
TitleTubulin-RB3_SLD-TTL in complex with compound 5l
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 / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Recruitment of NuMA to mitotic centrosomes / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / COPI-mediated anterograde transport / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / mitotic cell cycle / growth cone / microtubule / neuron projection / nucleotide binding / GTPase activity / 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. / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / 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-Y5L / 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: 2.9 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
DepositionMay 18, 2020Deposition 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)265,07722
Polymers261,3056
Non-polymers3,77216
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.360, 157.742, 182.163
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 , 8 types, 125 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine 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-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#9: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-Y5L / 4-(2-chloro-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl)-7-methoxy-3,4-dihydroquinoxalin-2(1H)-one


Mass: 330.769 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H15ClN4O2 / Feature type: SUBJECT OF INVESTIGATION
#11: 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
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 57.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 6% PEG 4000, 5% glycerol, 0.1M 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: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 67407 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 50.65 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.05 / Net I/σ(I): 15.7
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.137 / Mean I/σ(I) obs: 3 / Num. unique obs: 3331 / CC1/2: 0.804 / Rpim(I) all: 0.317 / % possible all: 99.8

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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: 2.9→49.91 Å / SU ML: 0.3518 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.8234 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2242 1996 2.98 %
Rwork0.17 64962 -
obs0.1717 66958 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17170 0 232 109 17511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002517820
X-RAY DIFFRACTIONf_angle_d0.544724170
X-RAY DIFFRACTIONf_chiral_restr0.04142624
X-RAY DIFFRACTIONf_plane_restr0.00383126
X-RAY DIFFRACTIONf_dihedral_angle_d17.012510655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.32381240.244036X-RAY DIFFRACTION86.99
2.97-3.060.26961410.22934582X-RAY DIFFRACTION98.83
3.06-3.150.29161420.21534621X-RAY DIFFRACTION99.73
3.15-3.250.28151420.21514636X-RAY DIFFRACTION99.9
3.25-3.360.29771430.2064650X-RAY DIFFRACTION99.98
3.36-3.50.28751440.19484665X-RAY DIFFRACTION99.98
3.5-3.660.23881440.17674678X-RAY DIFFRACTION100
3.66-3.850.21261430.16144639X-RAY DIFFRACTION100
3.85-4.090.20231430.14924685X-RAY DIFFRACTION100
4.09-4.410.19531460.13914711X-RAY DIFFRACTION100
4.41-4.850.18051440.12354704X-RAY DIFFRACTION100
4.85-5.550.21471460.14544739X-RAY DIFFRACTION100
5.55-6.990.20541470.18154778X-RAY DIFFRACTION99.9
6.99-49.910.18211470.17044838X-RAY DIFFRACTION97.21
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)
10.722989044603-0.02029740473120.1341564352412.177473425951.126900134131.962104005420.0140103951069-0.0185920686142-0.0421741867516-0.0817673387560.188434052273-0.1820921851410.2530545486080.262222133919-0.2012431160230.2635440678390.0156636308634-0.02498521140010.327304602835-0.1249023388910.33694344040825.5153257063-83.2381820188-61.6037757164
20.7636174452910.4564166459170.3737072465291.526303185230.9046483142291.98662930380.0862710756987-0.00865194719188-0.1395753201540.0163874084914-0.0554969005370.05250863177980.212751767705-0.0953877903201-0.07817946049230.1660115367210.00326841952602-0.03117896668440.299043299257-0.09033422973030.34166356876215.7999442506-57.5017213475-29.3714896579
30.7760131489660.161477193074-0.02445587139211.222960469540.2365064556371.32956932697-0.0638829160031-0.116372988724-0.03902007596220.09265513604520.02474788496520.04356667906250.000424323831998-0.09006108571890.02409983859880.1611935604520.05815046183080.006819197457270.243969307978-0.03263604148020.24639577352813.0380825588-29.22636197993.65216722303
41.36468976545-0.0825018035080.3042403374161.433981953570.1663794379741.82517022501-0.373594512391-0.6544042371350.2253055147650.4813264148780.2501176035760.0299986236855-0.39369903612-0.2462691900950.05631157220590.6110854695120.208991537559-0.09286375313160.621993769582-0.2170607558670.36526499321818.29196235951.8594362783431.5975858922
50.2399283749840.07134186790240.1970434310330.8768863034320.790395022941.07861061359-0.1028253572080.0527455319213-0.00693288482796-0.3711624626420.512300184384-0.462602624087-0.4420561803690.679481134269-0.3593283536870.321390312067-0.0433965359094-0.01100211855290.552578374213-0.194746276340.54141690128239.7792083031-40.9298436496-20.1743641221
61.19216780311-0.09631885918851.377770436091.05345869207-0.2327855520351.79469581686-0.3384950873290.3348489198360.539514370334-0.3754047297720.0969322967158-0.0593709180042-0.5663220338530.246713835154-0.003425414053180.790952629831-0.118243235229-0.1693638965960.4407474725850.08275186081320.5626625833944.19891494254-55.7358122628-91.8855161243
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 2 through 428)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 440)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 431)
5X-RAY DIFFRACTION5(chain 'E' and resid 6 through 141)
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 380)

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