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- PDB-6xes: Tubulin-RB3_SLD in complex with compound 40a -

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Basic information

Entry
Database: PDB / ID: 6xes
TitleTubulin-RB3_SLD in complex with compound 40a
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-TU3 / 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: 2.32 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)214,87316
Polymers211,7095
Non-polymers3,16411
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19810 Å2
ΔGint-136 kcal/mol
Surface area65390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.178, 126.966, 250.155
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 , 7 types, 243 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: 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
#7: Chemical ChemComp-TU3 / [6-(3-hydroxy-4-methylphenyl)pyrazin-2-yl](3,4,5-trimethoxyphenyl)methanone


Mass: 380.394 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H20N2O5 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / 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: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 89968 / % possible obs: 99.2 % / Redundancy: 8.4 % / Biso Wilson estimate: 45.16 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.043 / Net I/σ(I): 19.3
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5276 / CC1/2: 0.849 / Rpim(I) all: 0.276 / % possible all: 93.9

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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: 2.32→46.55 Å / SU ML: 0.2888 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.3149 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2255 2000 2.23 %
Rwork0.1714 87865 -
obs0.1726 89865 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.26 Å2
Refinement stepCycle: LAST / Resolution: 2.32→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14438 0 200 232 14870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007214952
X-RAY DIFFRACTIONf_angle_d0.893120277
X-RAY DIFFRACTIONf_chiral_restr0.05142205
X-RAY DIFFRACTIONf_plane_restr0.00562634
X-RAY DIFFRACTIONf_dihedral_angle_d18.83088928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.380.33351060.27814665X-RAY DIFFRACTION73.37
2.38-2.440.33711410.25766161X-RAY DIFFRACTION97.09
2.44-2.520.33521420.23156252X-RAY DIFFRACTION98.96
2.52-2.60.25471430.21396280X-RAY DIFFRACTION98.95
2.6-2.690.27091440.2076340X-RAY DIFFRACTION99.78
2.69-2.80.25761450.21146356X-RAY DIFFRACTION99.71
2.8-2.930.26021440.19876363X-RAY DIFFRACTION99.89
2.93-3.080.27641450.19396355X-RAY DIFFRACTION99.83
3.08-3.270.27231470.19056424X-RAY DIFFRACTION99.89
3.27-3.530.2261460.17516417X-RAY DIFFRACTION100
3.53-3.880.20231460.15276450X-RAY DIFFRACTION100
3.88-4.440.19661480.13926472X-RAY DIFFRACTION99.95
4.44-5.590.20831490.14056528X-RAY DIFFRACTION99.96
5.59-46.550.17231540.15896802X-RAY DIFFRACTION99.91
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)
16.5311654944-0.358747067943-0.4730401449224.02994766415-0.6898697381765.948122507320.199981840976-0.7963703262140.1727677822570.660733595883-0.1453889290140.555418398404-0.396050907353-0.958058982207-0.07597742997770.506982323876-0.03427845041860.05910902489160.540913443878-0.0934902562170.35245013001723.996922618886.377308712821.6064361656
24.49272303590.513439776554-2.695110022771.104605122130.4331161456843.372534769350.333259107115-0.6103858026610.7218664115210.396864150561-0.287795058319-0.0238756422765-0.7012441814530.425944951049-0.02141599059240.761171634225-0.197824881149-0.1276174366010.498792787031-0.02269438835730.53406228283642.309310304990.875953596720.9354795875
32.46072477010.61794965307-0.08818440073562.6219727076-0.8052835077772.959763747250.178417514116-0.196120817164-0.09481827891210.239319531841-0.239214226743-0.1008774254150.06466089440150.1480757664370.05105227963720.24379542157-0.0531519334767-0.0248410541980.2836383767210.02285030770510.30889395193638.060046671481.99873253368.19504213012
43.00964827377-3.945701210391.202351263147.726560679380.4715949135243.623451265890.0441704629508-0.2659319532680.0376935368240.28578094235-0.1461090238310.2052969703860.372453956837-0.3867326187450.1030437444910.292094748126-0.123792351163-0.0255570307940.3740282299450.02103062038520.29225777413828.233092175670.205415970511.6577067451
53.038457712230.642000161106-1.087555226651.475617446340.05216501254251.784654566280.03393104013480.3901325328720.353992245647-0.3703142951820.00242143995640.5939339402940.0258456252927-0.6424459211170.002478476574280.4179087721390.0235670554934-0.1199779967110.4815774535880.06031194405640.48796420834121.337314145579.2993775501-4.05153236637
67.58812882424-0.9276549115281.185810851078.244972759531.385558770894.54993224182-0.2317422875090.318132881881-0.374056154508-0.236429706069-0.2163549879131.369956699580.303215624009-1.023548729230.4500554676180.376068251418-0.116458391079-0.01508856121240.4972392481130.03589578625030.45690823761315.80205257468.27753694811.61707054808
74.9509880402-3.15427202895-1.462018677797.356939246770.890136033982.33809986752-0.01219178742190.09845723786060.038266501476-0.126336705749-0.05033942989770.3973883975250.277416853136-0.2412193205110.06341491287070.405374241017-0.135407583635-0.04914449864640.4173515256840.04231638586710.33961058926720.988395613668.64207314652.95148778702
84.85563706310.3649623305520.747146960483.196284306660.4341778439161.50105982949-0.1998469215960.906325964532-0.00383728623451-0.1412090518750.223683423763-0.2770197731970.143181367356-0.0533570835785-0.02204488115140.3499716723650.00381024070524-0.02512555347310.3219217190670.08079441632730.25889787200941.304421381676.2017993814-2.83374089802
95.237835409974.574718421281.047622398615.422498666031.142756885511.706075375490.18503568354-0.00853938594611-0.788679056330.029115494013-0.162122444036-1.255739820580.2863190911150.134025458147-0.04807617759920.386922226490.08166324656030.00635532363340.335048747970.1246215045430.53255745605751.82745009572.96669798051.43256280031
102.94835038838-0.543296702848-0.4306854045713.352031728250.4918320027163.71844425891-0.392896139156-0.0616256129064-0.6626908850310.32046406033-0.0284472036554-0.07324697500941.161895993270.005736462023460.4778400322150.92458642588-0.008415854970990.02162052038570.4883175841690.03015125379420.569053462623-11.1514528803-54.592649049551.9386565141
111.3476067763.22662831202-1.394452503234.92369259166-2.322149710160.8248282497740.231460069893-0.236645259843-0.456548061740.493527688198-0.601181647003-1.06728983718-0.1809933280940.3829290441150.3003013091430.916113660704-0.191758236973-0.1504282528740.7292029030470.2750804874540.88523036614935.442750346931.921385455135.8740850415
125.452016502081.3226447584-0.978221306183.561964248390.1525221174235.218098200730.0204072440029-0.543158731569-0.1790176921690.449116983684-0.1231542941290.3118426405030.287691990695-0.2488117831640.100037032960.568902958361-0.0295876074650.005142796430580.341569739228-0.003006528095190.306140933955-17.6443364173-27.991777595164.999942864
132.721010398110.956266275203-2.34345138923.70252278519-0.8782092839034.792219681250.0738176590883-0.3050263055220.02188429353630.333246113787-0.125664212429-0.0343318602367-0.3583762262680.1288156871060.05191423752620.5118617774350.00116220900871-0.05402735951780.3288958734080.02592704359790.273599417979-3.0219526974-22.292133907656.3252397083
142.57742520648-0.09786301184-0.0005426806028113.690237420570.2357370997332.38571438368-0.04947336766350.232196277241-0.183831985124-0.3079638945370.001577761931620.337665080160.36310171528-0.2954753394670.04852016737590.595795274719-0.0723476060435-0.03147811649760.4452675925440.01588199999530.345691295168-18.1350778944-39.645208756245.9860660762
151.742281519981.87349335166-0.8435870582183.78264041407-1.132930567530.952353036231-0.1516767404180.0584807417278-0.249326840074-0.506073026684-0.0666180535637-0.4486368846020.3119128482040.08638293165390.1895723076860.5620808470280.06414277491990.03432063170740.369358626690.04631349828170.3336811845723.15077242543-29.541475974738.9173090257
162.811709866680.9128250061210.1255821393972.71579448682-0.06119923289522.264061101050.0969979059791-0.3122067113410.3617989799670.43823127894-0.1144676882520.357697367374-0.236319391133-0.1752767551560.01408387279320.6367714133390.006704956077280.0287468887910.351104077833-0.02680657537590.422320082351-2.3785803027313.165331818739.7917052941
179.76426301831-4.077401225270.9904894668965.198279879652.219647410782.92841340144-0.000760348879163-0.3435991043420.1564090262440.0353353167322-0.09236413113470.3641065909610.2120666190450.1041661521170.08756651061970.509828660562-0.118054961246-0.03703678620160.2780697029330.006041303157960.331089019677-2.29602612784-4.4297531413336.8946208279
181.212106247931.03897046884-0.4231115544693.23707504408-0.2831422205170.910688750188-0.1741559593810.194249662321-0.0223409492409-0.2798228741680.1730940020650.2023420931650.137477205448-0.186633840925-0.007577868388630.515269496099-0.0311582265113-0.04129350156810.3690692693940.06261319560120.266226545248-1.49640719563-0.1635489964225.2209136157
193.081843326980.206474016053-1.091693423542.56664283443-0.3190717340273.30073395911-0.0514566393821-0.1594327673150.08930694210490.512450305618-0.06245144391060.225845606692-0.250526518461-0.1280348627010.108822013170.586495437086-0.07101648175380.007337054440310.3141550299350.01559007563290.32831245615716.41581277751.3375823231.3133490622
203.08105952954-1.4798033401-0.4285416230285.99780343460.2451128330791.51998934739-0.1514773599240.1031994501430.0661485783895-0.121572035412-0.02143237833350.4784913387620.353638939479-0.3384220930080.1251816852130.423139461993-0.10566148468-0.0184254761460.408660466301-0.01084835652460.3925651330757.6945189867243.779423929919.6909658453
212.470781185961.73059279981-0.505857113932.18381110964-0.4839664901690.695403254451-0.1317752733570.1490523349630.0485260233307-0.2650843838660.1137965382450.2306089804520.168959063536-0.2454851150690.03620961573730.532652103975-0.0483074697345-0.03348716240550.4072872256640.04904127633440.34852661120510.887643110339.066175684313.4935351042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 62 )
2X-RAY DIFFRACTION2chain 'D' and (resid 63 through 125 )
3X-RAY DIFFRACTION3chain 'D' and (resid 126 through 236 )
4X-RAY DIFFRACTION4chain 'D' and (resid 237 through 271 )
5X-RAY DIFFRACTION5chain 'D' and (resid 272 through 309 )
6X-RAY DIFFRACTION6chain 'D' and (resid 310 through 336 )
7X-RAY DIFFRACTION7chain 'D' and (resid 337 through 362 )
8X-RAY DIFFRACTION8chain 'D' and (resid 363 through 391 )
9X-RAY DIFFRACTION9chain 'D' and (resid 392 through 431 )
10X-RAY DIFFRACTION10chain 'E' and (resid 6 through 46 )
11X-RAY DIFFRACTION11chain 'E' and (resid 47 through 140 )
12X-RAY DIFFRACTION12chain 'A' and (resid 1 through 64 )
13X-RAY DIFFRACTION13chain 'A' and (resid 65 through 199 )
14X-RAY DIFFRACTION14chain 'A' and (resid 200 through 372 )
15X-RAY DIFFRACTION15chain 'A' and (resid 373 through 437 )
16X-RAY DIFFRACTION16chain 'B' and (resid 1 through 241 )
17X-RAY DIFFRACTION17chain 'B' and (resid 242 through 271 )
18X-RAY DIFFRACTION18chain 'B' and (resid 272 through 430 )
19X-RAY DIFFRACTION19chain 'C' and (resid 1 through 197 )
20X-RAY DIFFRACTION20chain 'C' and (resid 198 through 273 )
21X-RAY DIFFRACTION21chain 'C' and (resid 274 through 438 )

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