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- PDB-7lz7: Tubulin-RB3_SLD-TTL in complex with compound 5k -

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Basic information

Entry
Database: PDB / ID: 7lz7
TitleTubulin-RB3_SLD-TTL in complex with compound 5k
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 / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle ...tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / EML4 and NUDC in mitotic spindle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / microtubule depolymerization / 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 / COPI-mediated anterograde transport / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / mitotic cell cycle / microtubule cytoskeleton / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm
Similarity search - Function
Rossmann fold - #11480 / Helix hairpin bin / 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. ...Rossmann fold - #11480 / Helix hairpin bin / 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/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / 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 / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-YJ7 / 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: 2.8 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)265,06622
Polymers261,3056
Non-polymers3,76116
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.211, 157.998, 182.056
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, 151 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-YJ7 / 4-(3,6-dimethyl[1,2]oxazolo[5,4-d]pyrimidin-4-yl)-7-methoxy-3,4-dihydroquinoxalin-2(1H)-one


Mass: 325.322 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H15N5O3 / Feature type: SUBJECT OF INVESTIGATION
#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-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


Mass: 18.015 Da / Num. of mol.: 135 / 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: 57.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7 / Details: PEG 4000, glycerol, MES, CaCl2, MgCl2

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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: 2.8→50 Å / Num. obs: 75636 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 45.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.053 / Net I/σ(I): 14.6
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3739 / CC1/2: 0.749 / Rpim(I) all: 0.339 / % possible all: 100

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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: 2.8→49.88 Å / SU ML: 0.295 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.9969 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2111 1995 2.68 %
Rwork0.1712 72555 -
obs0.1723 74550 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.84 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17191 0 234 135 17560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002317805
X-RAY DIFFRACTIONf_angle_d0.553824145
X-RAY DIFFRACTIONf_chiral_restr0.04162623
X-RAY DIFFRACTIONf_plane_restr0.00383121
X-RAY DIFFRACTIONf_dihedral_angle_d17.998210626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.32331270.25864638X-RAY DIFFRACTION89.55
2.87-2.950.30011380.23295017X-RAY DIFFRACTION97.5
2.95-3.030.30751430.21495158X-RAY DIFFRACTION99.2
3.03-3.130.23951410.21495162X-RAY DIFFRACTION99.92
3.13-3.240.271430.20445181X-RAY DIFFRACTION99.96
3.24-3.370.2291430.19595199X-RAY DIFFRACTION99.98
3.37-3.530.25081420.18685192X-RAY DIFFRACTION100
3.53-3.710.23171440.17185232X-RAY DIFFRACTION100
3.71-3.950.19481440.15455210X-RAY DIFFRACTION100
3.95-4.250.16961430.13975234X-RAY DIFFRACTION100
4.25-4.680.16151440.12735257X-RAY DIFFRACTION100
4.68-5.350.17121460.13745273X-RAY DIFFRACTION100
5.35-6.740.21051470.17935340X-RAY DIFFRACTION100
6.74-49.880.17891500.16855462X-RAY DIFFRACTION98.77
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)
10.77995995574-0.004682672973980.1311158959612.113001600871.150034935152.100715711590.0362532392318-0.0248621727199-0.0526023895579-0.03903596104450.164212237371-0.1719650047120.2878640190220.248508525081-0.2051731547220.2698367549880.0287698779402-0.02896684584890.308246180036-0.1119399514960.32124105789325.4764768851-83.4032233206-61.6083566744
20.7703777859320.4358652736220.1846546233051.424619676590.7900374146432.105392582950.05739356860160.0201691107919-0.1316706075450.00578683164895-0.0472099259710.02143404113960.215798814594-0.132865327219-0.08375728043080.1333067996280.00535739612197-0.02480112036720.268899535024-0.08871465794120.31213577496815.8594355272-57.6050294827-29.3576461546
30.6576918722240.062441508077-0.04142604318841.121875567040.4101729184781.14957156046-0.0450286706498-0.10447749959-0.04490815896820.1055313579360.007008818061090.05441832292550.0190125946375-0.07354066409820.02762969945240.1742100327130.04804579310590.006097788622950.256190304564-0.02001575619780.24732565639113.1283966837-29.20187433243.68149694205
41.35479101887-0.1648171696510.3703220570541.390692425520.3346633748472.00142870867-0.248824748942-0.5807299978860.2325354665260.3844714690170.169675631534-0.00320187691339-0.304177375078-0.2070894717070.04110635146620.5300303043360.146387336608-0.07875917796620.534860871082-0.2038985871240.33633100692518.33247054071.8592554426531.6916955352
50.2218092491220.173403596590.2790945004040.7696465346660.6608312374151.0172109302-0.09382908399490.0487375144451-0.0026143212713-0.2978936645340.423949572156-0.383526537304-0.3571600044140.584319015647-0.3742271445920.289179113545-0.0307656864208-0.01569530743780.539143205398-0.1815709389180.5007716823539.8356685098-41.3214520751-20.5309363938
61.52224223705-0.02312873248491.593650733871.40538194472-0.3760773392162.21258744166-0.4032460346740.3255638973480.557912161493-0.3042520867710.0989670985626-0.129268474417-0.6435585946660.220669806146-0.00311645209140.707574421539-0.087451284093-0.1367254348790.3539704007140.0668898817480.5411885595934.32587671741-55.7159615171-92.0270535614
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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