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- PDB-6x1f: Tubulin-RB3_SLD-TTL in complex with compound 5m -

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Basic information

Entry
Database: PDB / ID: 6x1f
TitleTubulin-RB3_SLD-TTL in complex with compound 5m
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 / 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 / microtubule depolymerization / 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 / microtubule cytoskeleton / 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
Rossmann fold - #11480 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Helix hairpin bin / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. ...Rossmann fold - #11480 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Helix hairpin bin / 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 / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 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-Y5M / 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: 2.7 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)264,98720
Polymers261,3056
Non-polymers3,68214
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.480, 157.923, 182.205
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, 294 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.: 3 / Source method: obtained synthetically / Formula: Mg
#8: 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
#9: 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
#10: Chemical ChemComp-Y5M / 7-methoxy-4-(2-methyl-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl)-3,4-dihydroquinoxalin-2(1H)-one


Mass: 310.350 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18N4O2 / 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


Mass: 18.015 Da / Num. of mol.: 280 / 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: 57.64 %
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: Jul 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 84115 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 41.02 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.045 / Net I/σ(I): 17.5
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4130 / CC1/2: 0.592 / % 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: 2.7→48.24 Å / SU ML: 0.337 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 24.5364 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2408 2000 2.47 %
Rwork0.1903 78919 -
obs0.1915 80919 96.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.9 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17142 0 230 280 17652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002117781
X-RAY DIFFRACTIONf_angle_d0.532324115
X-RAY DIFFRACTIONf_chiral_restr0.0412619
X-RAY DIFFRACTIONf_plane_restr0.00373118
X-RAY DIFFRACTIONf_dihedral_angle_d17.832410629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.3132910.28253605X-RAY DIFFRACTION62.24
2.77-2.840.34331290.26375083X-RAY DIFFRACTION87.8
2.84-2.930.28811440.25055687X-RAY DIFFRACTION97.8
2.93-3.020.331470.24395770X-RAY DIFFRACTION99.68
3.02-3.130.26311460.23965771X-RAY DIFFRACTION99.81
3.13-3.250.2881470.22165802X-RAY DIFFRACTION99.95
3.25-3.40.26131480.20855833X-RAY DIFFRACTION100
3.4-3.580.23881470.19215825X-RAY DIFFRACTION99.98
3.58-3.810.25481480.17955819X-RAY DIFFRACTION100
3.81-4.10.21351480.16245856X-RAY DIFFRACTION99.8
4.1-4.510.19931480.1475876X-RAY DIFFRACTION100
4.51-5.160.19161500.14575896X-RAY DIFFRACTION99.9
5.16-6.50.25761510.18795943X-RAY DIFFRACTION99.89
6.5-48.240.20691560.18296153X-RAY DIFFRACTION99.4
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)
10.947614352238-0.06749352610280.1956462359812.310526671171.282404557892.190606042930.0400812305240.0237050720492-0.101314310458-0.04700779208060.258141749409-0.2437501660130.3164957022230.317228320209-0.2430806961290.2592187684270.036283130142-0.03777432678210.2946573448-0.1469441991420.30762806351425.5885558799-83.4422847871-61.5825997301
20.7248683666920.4692040530430.3409293324831.748768136471.125091710212.245257763920.0540876446582-0.013503446723-0.142553879680.0767871163907-0.01375501576310.06162995233760.254888009412-0.0796848743047-0.09570265465960.1126065408340.0115679936182-0.02740170031420.23769304421-0.07715087917890.28163819038615.6770217763-57.7731605213-29.2847504522
30.8103739596890.163422443288-0.09863207207941.323612031370.432215852371.54448336315-0.0835487380807-0.144168243468-0.03862961251320.132288604160.02015179552830.0803404601090.0227603728621-0.09501635628910.03169689624360.1371932934440.0645507666966-0.003652849161140.223678909849-0.03702507263650.22221999617612.9776795601-29.26731260773.62512645366
41.47063247427-0.1136374708040.3475345060971.546603069180.4066466929021.99746652957-0.467492904466-0.8192444397570.261398515690.5050092862190.3790887547930.0761422667555-0.467901041197-0.2917090842910.067902120270.644180326920.301037374937-0.1379078124520.648880932625-0.3190699616570.2849055043618.18788771811.8931483665331.3855193837
50.3081815415760.2181016524130.3295966163160.9083362982360.7175179934091.12815149645-0.04993265981910.0634252561235-0.0423214040603-0.315908235530.544627035111-0.589776907252-0.4084151756390.709665163632-0.3104659077460.220003136391-0.0241336757165-0.04210427601850.551409750791-0.2515931473090.47977442064739.718121318-41.1772039601-20.3513085684
61.33423816772-0.1765662053991.512053094911.1291753447-0.2923780240822.00490043151-0.3523696605890.3673728034160.544376421735-0.3993328129720.113918982159-0.0536106553411-0.6782066042790.2597927704830.01190974655470.793625612025-0.117022638159-0.1668088600230.3964270251460.1005065784120.5224968277244.12508986141-56.0732674692-91.5486460299
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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