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- PDB-7z02: Z-SBTub2M photoswitch bound to tubulin-DARPin D1 complex -

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Basic information

Entry
Database: PDB / ID: 7z02
TitleZ-SBTub2M photoswitch bound to tubulin-DARPin D1 complex
Components
  • Designed Ankyrin Repeat Protein (DARPIN) D1
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE / microtubule dynamics / cytoskeleton / photopharmacology / tubulin polymerisation inhibitor / optical control / colchicine / antimitotic / cell division / cell migration / development / photoswitch
Function / homology
Function and homology information


positive regulation of axon guidance / cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / double-stranded RNA binding / mitotic cell cycle ...positive regulation of axon guidance / cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / double-stranded RNA binding / mitotic cell cycle / nervous system development / microtubule / protein heterodimerization activity / GTPase activity / ubiquitin protein ligase binding / GTP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / 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-beta mRNA autoregulation signal. / Alpha tubulin / 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-I8N / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciessynthetic construct (others)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsWranik, M. / Weinert, T. / Standfuss, J. / Steinmetz, M.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_197674 Switzerland
Swiss National Science Foundation31003A_179351 Switzerland
Swiss National Science Foundation310030_192566 Switzerland
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: In Vivo Photocontrol of Microtubule Dynamics and Integrity, Migration and Mitosis, by the Potent GFP-Imaging-Compatible Photoswitchable Reagents SBTubA4P and SBTub2M.
Authors: Gao, L. / Meiring, J.C.M. / Varady, A. / Ruider, I.E. / Heise, C. / Wranik, M. / Velasco, C.D. / Taylor, J.A. / Terni, B. / Weinert, T. / Standfuss, J. / Cabernard, C.C. / Llobet, A. / ...Authors: Gao, L. / Meiring, J.C.M. / Varady, A. / Ruider, I.E. / Heise, C. / Wranik, M. / Velasco, C.D. / Taylor, J.A. / Terni, B. / Weinert, T. / Standfuss, J. / Cabernard, C.C. / Llobet, A. / Steinmetz, M.O. / Bausch, A.R. / Distel, M. / Thorn-Seshold, J. / Akhmanova, A. / Thorn-Seshold, O.
History
DepositionFeb 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: 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 1.2Jan 31, 2024Group: 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
F: Designed Ankyrin Repeat Protein (DARPIN) D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,6318
Polymers118,2733
Non-polymers1,3585
Water1629
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.683, 91.615, 83.110
Angle α, β, γ (deg.)90.000, 97.390, 90.000
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 natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (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 coli BL21 (bacteria)

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Non-polymers , 5 types, 14 molecules

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


Mass: 523.180 Da / Num. of mol.: 1 / 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-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine 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-I8N / 6-methyl-2-[2-(3,4,5-trimethoxyphenyl)ethyl]-1,3-benzothiazole


Mass: 343.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21NO3S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium sulfate, 0.1M Bis/Tris-methane pH=5.5, 21% PEG 3000 (m/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36→45.81 Å / Num. obs: 27889 / % possible obs: 92.9 % / Redundancy: 11.7 % / CC1/2: 0.974 / Net I/σ(I): 4.7
Reflection shellResolution: 2.36→2.69 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1330 / CC1/2: 0.517

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NQT

5nqt


Resolution: 2.36→45.81 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 1994 7.15 %
Rwork0.2046 25895 -
obs0.2084 27889 61.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.66 Å2 / Biso mean: 57.2204 Å2 / Biso min: 13 Å2
Refinement stepCycle: final / Resolution: 2.36→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7870 0 124 9 8003
Biso mean--52.84 36.39 -
Num. residues----1023
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.36-2.420.369290.35621151244
2.42-2.490.2871180.33472362548
2.49-2.560.4747330.351942946214
2.56-2.640.3713440.3557561919
2.64-2.740.3726640.352181988327
2.74-2.840.4107950.30811234132942
2.85-2.970.31391520.31011986213867
2.97-3.130.34111920.29722491268384
3.13-3.330.32292260.26852936316298
3.33-3.580.27772300.232229853215100
3.58-3.940.27782310.188930043235100
3.94-4.520.22692310.158629973228100
4.52-5.680.20612320.158330143246100
5.69-45.810.2092370.170830743311100
Refinement TLS params.Method: refined / Origin x: 14.9084 Å / Origin y: -15.3925 Å / Origin z: 14.7946 Å
111213212223313233
T0.1916 Å2-0.0086 Å20.0215 Å2-0.0425 Å20.0008 Å2--0.1762 Å2
L0.4835 °20.0546 °2-0.245 °2-0.0115 °2-0.0449 °2--0.2756 °2
S0.0126 Å °0.0766 Å °-0.1844 Å °0.018 Å °-0.0376 Å °-0.0027 Å °-0.059 Å °-0.046 Å °-0.0075 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 502
2X-RAY DIFFRACTION1allB1 - 601
3X-RAY DIFFRACTION1allF13 - 167
4X-RAY DIFFRACTION1allC1
5X-RAY DIFFRACTION1allD1 - 9

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