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- PDB-6xer: Tubulin-RB3_SLD in complex with colchicine -

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Basic information

Entry
Database: PDB / ID: 6xer
TitleTubulin-RB3_SLD in complex with colchicine
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsCELL CYCLE/INHIBITOR / MICROTUBULE INHIBITOR / COLCHICINE / CELL CYCLE / CANCER / CELL CYCLE-INHIBITOR COMPLEX
Function / homology
Function and homology information


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 ...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 / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / microtubule depolymerization / COPI-mediated anterograde transport / regulation of microtubule polymerization or depolymerization / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / mitotic cell cycle / growth cone / microtubule / neuron projection / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm
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
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-LOC / Tubulin beta chain / Stathmin-4 / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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: Design, Synthesis, and Biological Evaluation of Stable Colchicine-Binding Site Tubulin Inhibitors 6-Aryl-2-benzoyl-pyridines as Potential Anticancer Agents.
Authors: Chen, H. / Deng, S. / Albadari, N. / Yun, M.K. / Zhang, S. / Li, Y. / Ma, D. / Parke, D.N. / Yang, L. / Seagroves, T.N. / White, S.W. / Miller, D.D. / Li, W.
History
DepositionJun 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 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 chain
C: Tubulin alpha-1B chain
D: Tubulin beta chain
E: Stathmin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,85716
Polymers211,7095
Non-polymers3,14811
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19500 Å2
ΔGint-140 kcal/mol
Surface area64840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.717, 127.025, 254.208
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 , 3 types, 5 molecules ACBDE

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 48780.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta chain


Mass: 48648.652 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: 16851.133 Da / Num. of mol.: 1 / Mutation: C14A, F20W
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

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Non-polymers , 6 types, 40 molecules

#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: 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
#8: Chemical ChemComp-LOC / N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide / COLCHICINE


Mass: 399.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25NO6 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antiinflammatory*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6 / Details: PEG 4000, ammonium sulfate, tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 75107 / % possible obs: 99.7 % / Redundancy: 4.6 % / Biso Wilson estimate: 62.23 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.058 / Net I/σ(I): 16.6
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.911 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4642 / CC1/2: 0.646 / Rpim(I) all: 0.505 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XIW

5xiw


Resolution: 2.5→38.34 Å / SU ML: 0.2885 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.0623 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2226 1983 2.66 %
Rwork0.1681 72432 -
obs0.1696 74415 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.22 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14378 0 199 29 14606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007514890
X-RAY DIFFRACTIONf_angle_d0.933420194
X-RAY DIFFRACTIONf_chiral_restr0.05162195
X-RAY DIFFRACTIONf_plane_restr0.00572628
X-RAY DIFFRACTIONf_dihedral_angle_d18.9688925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.32081390.27515102X-RAY DIFFRACTION99.7
2.56-2.630.27661410.25015119X-RAY DIFFRACTION99.64
2.63-2.710.28691390.23955081X-RAY DIFFRACTION99.77
2.71-2.80.25491390.22355106X-RAY DIFFRACTION99.68
2.8-2.90.28661410.21295127X-RAY DIFFRACTION99.87
2.9-3.010.25061410.20195132X-RAY DIFFRACTION99.89
3.01-3.150.25611410.19745156X-RAY DIFFRACTION99.89
3.15-3.320.29121400.19695146X-RAY DIFFRACTION99.89
3.32-3.520.25421420.1855147X-RAY DIFFRACTION99.89
3.52-3.790.2081410.16435184X-RAY DIFFRACTION99.94
3.79-4.180.20151430.14865212X-RAY DIFFRACTION99.93
4.18-4.780.18041420.12925211X-RAY DIFFRACTION99.37
4.78-6.020.20651450.15665268X-RAY DIFFRACTION99.5
6.02-38.340.20281490.14995441X-RAY DIFFRACTION98.76
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)
11.819714137420.7943650916750.0093513127912.51899008752-0.1456596807971.577030826710.00429410526314-0.161807374190.2491360286720.159349320486-0.1032558267060.126039497098-0.053039398257-0.08395535562270.1002354054760.350731909930.01878048201070.01577516962560.3844836240220.04298478438760.40770992548832.07808542579.46376006518.77937502395
20.7677959708891.68779108113-0.7524775740824.15452915214-1.518140371320.601753968830.0102562526245-0.0729824843516-0.2917607207370.0738006032667-0.210018013501-0.549439533794-0.04103615017850.1344725637530.2189933802370.869496669392-0.05383746078-0.01930694905820.9053103650450.20753537820.93821200152725.156296069714.430611802939.303586336
31.666077115270.702347908658-0.6343517923453.09715950671-0.7346268879732.00226442653-0.0439455648847-0.103607227851-0.2378929537510.0354149768292-0.04107372582620.2150781821270.320586927611-0.06516274868070.08979118986250.5735316500020.04280084166060.06354724559990.4903430653620.08451351110720.436825743292-10.5528330676-31.01569107851.9137386211
41.769337713341.28921044652-0.2354800524013.83746840573-0.4247338435571.202717837830.0442768667848-0.1215276953350.231805150511-0.0444872298146-0.03646289246650.458816272037-0.0625899368746-0.119757381985-0.008046581888530.5148643283090.03835004489610.01711774491720.4325368350780.01557295310730.401742364083-3.200683782226.7710993265435.0418356246
50.8867453148050.561191639195-0.2224246912151.76035341706-0.3417720023831.24281534090.0281221333584-0.1149553951050.07951798483740.184524633694-0.05072076926970.3824201988950.0944700770742-0.1900349237570.03570202614460.516812603669-0.0002876992736380.1200622723490.4358571848830.02684931163080.49734011486311.495676798745.375429060322.7125358346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'D' and resid 2 through 431)
2X-RAY DIFFRACTION2(chain 'E' and resid 7 through 140)
3X-RAY DIFFRACTION3(chain 'A' and resid 1 through 437)
4X-RAY DIFFRACTION4(chain 'B' and resid 1 through 430)
5X-RAY DIFFRACTION5(chain 'C' and resid 1 through 438)

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