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- PDB-9f8g: Photostatin (photoswitchable azo-combretastatin) Z-PST27 bound to... -

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Basic information

Entry
Database: PDB / ID: 9f8g
TitlePhotostatin (photoswitchable azo-combretastatin) Z-PST27 bound to tubulin-DARPin D1 complex
Components
  • Designed Ankyrin Repeat Protein (DARPIN) D1
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE / tubulin polymerisation inhibitor / microtubule dynamics / antimitotics / photopharmacology / photoswitch / sensitisation
Function / homology
Function and homology information


positive regulation of axon guidance / microtubule-based process / cytoplasmic microtubule / cellular response to interleukin-4 / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton ...positive regulation of axon guidance / microtubule-based process / cytoplasmic microtubule / cellular response to interleukin-4 / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cilium / protein heterodimerization activity / GTPase activity / ubiquitin protein ligase binding / GTP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
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 ...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'-TRIPHOSPHATE / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWranik, M. / Steinmetz, M.O.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166608 Switzerland
CitationJournal: Chem Sci / Year: 2024
Title: A photo-SAR study of photoswitchable azobenzene tubulin-inhibiting antimitotics identifying a general method for near-quantitative photocontrol.
Authors: Reynders, M. / Garscia, M. / Muller-Deku, A. / Wranik, M. / Krauskopf, K. / de la Osa de la Rosa, L. / Schaffer, K. / Jotten, A. / Rode, A. / Stierle, V. / Kraus, Y. / Baumgartner, B. / Ali, ...Authors: Reynders, M. / Garscia, M. / Muller-Deku, A. / Wranik, M. / Krauskopf, K. / de la Osa de la Rosa, L. / Schaffer, K. / Jotten, A. / Rode, A. / Stierle, V. / Kraus, Y. / Baumgartner, B. / Ali, A. / Bubeneck, A. / Seal, T. / Steinmetz, M.O. / Paulitschke, P. / Thorn-Seshold, O.
History
DepositionMay 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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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
F: Designed Ankyrin Repeat Protein (DARPIN) D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7069
Polymers118,2733
Non-polymers1,4336
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-60 kcal/mol
Surface area36020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.460, 91.115, 82.684
Angle α, β, γ (deg.)90.00, 97.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 3 molecules ABF

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


Mass: 50204.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Bos taurus (domestic cattle) / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: TUBB2B / Production host: Bos taurus (domestic cattle) / References: UniProt: Q6B856
#3: Protein Designed Ankyrin Repeat Protein (DARPIN) D1


Mass: 18068.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia phage EcSzw-2 (virus) / Strain (production host): BL21

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Non-polymers , 5 types, 171 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#7: Chemical ChemComp-A1IBN / 5-[(~{Z})-(3,5-diethyl-4-methoxy-phenyl)diazenyl]-2-methyl-phenol


Mass: 298.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N2O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.32 Å3/Da / Density % sol: 46.96 % / Description: Monoclinic needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 21% PEG 3000 (w/v), 0.2 M ammonium sulfate and 0.1 M bis-tris methane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.905→44.62 Å / Num. obs: 65942 / % possible obs: 78.16 % / Redundancy: 6.13 % / CC1/2: 0.9903 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.059 / Rrim(I) all: 0.148 / Net I/σ(I): 13.385
Reflection shellResolution: 1.905→2.032 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.837 / Num. unique obs: 3297 / CC1/2: 0.6969 / Rpim(I) all: 0.439 / Rrim(I) all: 0.846 / % possible all: 22.34

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→44.62 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 1619 2.96 %
Rwork0.1871 --
obs0.1883 54617 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7868 0 89 165 8122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038657
X-RAY DIFFRACTIONf_angle_d0.6111878
X-RAY DIFFRACTIONf_dihedral_angle_d13.5641291
X-RAY DIFFRACTIONf_chiral_restr0.0421321
X-RAY DIFFRACTIONf_plane_restr0.0041577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.25111310.2414265X-RAY DIFFRACTION97
2.26-2.340.26711340.23364421X-RAY DIFFRACTION99
2.34-2.420.27341340.22014373X-RAY DIFFRACTION100
2.42-2.520.28361360.21494457X-RAY DIFFRACTION100
2.52-2.630.21431340.19934400X-RAY DIFFRACTION100
2.63-2.770.2281360.20454437X-RAY DIFFRACTION100
2.77-2.950.27241360.20954449X-RAY DIFFRACTION100
2.95-3.170.22871340.20554418X-RAY DIFFRACTION100
3.17-3.490.21381340.19174374X-RAY DIFFRACTION99
3.49-40.20091360.16784446X-RAY DIFFRACTION100
4-5.030.18931360.14414467X-RAY DIFFRACTION100
5.03-44.620.23131380.1844491X-RAY DIFFRACTION99
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)
11.16350.79680.73322.561-0.572.94210.1584-0.06680.00130.0696-0.01540.30470.1087-0.8052-0.08460.25730.0046-0.01030.38980.03470.2355-19.2667-15.519331.6462
21.41270.4990.50491.45460.26132.07230.04530.0751-0.2982-0.0207-0.01160.00070.1862-0.5606-0.05990.2799-0.0098-0.02670.33670.04480.2307-14.2198-16.604721.3745
32.12320.1176-0.02290.87960.3462.12760.04020.05440.126-0.12250.0046-0.0433-0.3382-0.1233-0.02040.30070.0690.02960.1750.04560.2124-6.5797-2.631421.5013
41.462-0.2648-0.15021.29860.46072.71520.0223-0.16340.0443-0.08560.0757-0.0348-0.2276-0.1084-0.06380.29520.00440.00310.23010.03550.2397-4.1508-9.157938.8208
51.1717-0.5833-0.48060.88381.10152.80460.0592-0.3036-0.15020.0161-0.0612-0.36230.09040.1941-0.0480.311-0.0059-0.06080.25560.02930.28810.628-12.7850.5379
62.15330.8771-0.75391.9107-0.49112.3250.189-0.3606-0.04070.1859-0.0253-0-0.21520.0206-0.07610.33410.0499-0.01970.3303-0.02540.181-8.9409-4.875755.0114
71.5792-0.4444-0.37061.0704-0.25412.08590.0489-0.1707-0.14280.1234-0.1051-0.1521-0.1142-0.1226-0.07270.34070.0784-0.03430.35460.00250.2523-7.4665-7.740349.6678
81.10020.1376-0.5180.1334-0.34971.33250.1814-0.05210.17530.07920.033-0.0239-0.41740.1453-0.17390.3905-0.03190.07440.2052-0.02630.3028.38553.263428.6875
92.58570.9424-0.48722.123-0.99342.4176-0.0181-0.0771-0.6349-0.0070.02610.56990.1999-0.34720.06630.297-0.0423-0.0240.3452-0.06950.72999.0998-32.17832.9988
101.7790.1504-0.29141.2615-0.08341.52020.00580.4171-0.1649-0.1839-0.06810.28750.0804-0.180.03490.26520.012-0.08530.3323-0.08830.39419.7522-20.7587-5.8067
111.3316-0.34430.38492.1037-0.16940.92-0.1108-0.0731-0.46750.18830.01050.29250.2072-0.13180.10470.2748-0.00350.01610.2532-0.03440.425919.7539-25.94219.8987
122.2853-0.1111-1.10580.9255-0.15981.91290.0629-0.3031-0.08210.0785-0.04630.1542-0.0070.1245-0.03590.173-0.0189-0.03310.2179-0.020.237928.1914-16.321711.9452
133.75491.288-0.56715.5809-0.95743.9107-0.13130.38590.3904-0.28050.10490.5345-0.7621-0.65240.02950.4454-0.0366-0.05320.6405-0.08550.251950.2635-11.3751-29.2345
142.96681.6236-1.58063.1621-1.3714.59020.07220.2535-0.6689-1.237-0.0014-0.41380.3427-0.125-0.17220.8264-0.04790.06580.6794-0.16060.44654.1164-19.737-32.4267
151.92860.1711-0.35810.7042-0.21772.1458-0.05040.1295-0.1637-0.02170.0424-0.0620.0623-0.02890.02390.17870.0077-0.00340.2447-0.01610.204355.3664-15.6157-13.1102
163.0901-0.682-0.10344.68540.57743.20670.1384-0.2916-0.01560.1572-0.11910.0102-0.26240.15630.07440.2467-0.0047-0.03940.3164-0.00670.212156.5926-10.58913.8221
172.79580.43010.5874.3539-0.80713.2854-0.0223-0.0418-0.04060.44240.1371-0.17-0.1070.05890.00280.2935-0.0057-0.0340.36780.01470.263349.4162-19.93778.6114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 102 )
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 197 )
4X-RAY DIFFRACTION4chain 'A' and (resid 198 through 273 )
5X-RAY DIFFRACTION5chain 'A' and (resid 274 through 311 )
6X-RAY DIFFRACTION6chain 'A' and (resid 312 through 337 )
7X-RAY DIFFRACTION7chain 'A' and (resid 338 through 372 )
8X-RAY DIFFRACTION8chain 'A' and (resid 373 through 436 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 57 )
10X-RAY DIFFRACTION10chain 'B' and (resid 58 through 213 )
11X-RAY DIFFRACTION11chain 'B' and (resid 214 through 257 )
12X-RAY DIFFRACTION12chain 'B' and (resid 258 through 431 )
13X-RAY DIFFRACTION13chain 'F' and (resid 13 through 24 )
14X-RAY DIFFRACTION14chain 'F' and (resid 25 through 35 )
15X-RAY DIFFRACTION15chain 'F' and (resid 36 through 134 )
16X-RAY DIFFRACTION16chain 'F' and (resid 135 through 148 )
17X-RAY DIFFRACTION17chain 'F' and (resid 149 through 167 )

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