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- PDB-6zwc: Z-SBTub2 photoswitch bound to tubulin-DARPin D1 complex -

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Basic information

Entry
Database: PDB / ID: 6zwc
TitleZ-SBTub2 photoswitch bound to tubulin-DARPin D1 complex
Components
  • Designed Ankyrin Repeat Protein (DARPIN) D1
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE / photopharmacology / microtubule dynamics / cytoskeleton / tubulin polymerisation inhibitor / colchicine / antimitotic / azobenzene / cell division / spatiotemporal control
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-QRQ / 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: 2.04 Å
AuthorsWranik, M. / Weinert, T. / Olieric, N. / Gao, L. / Kraus, Y.C.M. / Bingham, R. / Ntouliou, E. / Ahlfeld, J. / Thorn-Seshold, O. / Steinmetz, M.O. / Standfuss, J.
CitationJournal: Cell Chem Biol / Year: 2021
Title: A Robust, GFP-Orthogonal Photoswitchable Inhibitor Scaffold Extends Optical Control over the Microtubule Cytoskeleton.
Authors: Gao, L. / Meiring, J.C.M. / Kraus, Y. / Wranik, M. / Weinert, T. / Pritzl, S.D. / Bingham, R. / Ntouliou, E. / Jansen, K.I. / Olieric, N. / Standfuss, J. / Kapitein, L.C. / Lohmuller, T. / ...Authors: Gao, L. / Meiring, J.C.M. / Kraus, Y. / Wranik, M. / Weinert, T. / Pritzl, S.D. / Bingham, R. / Ntouliou, E. / Jansen, K.I. / Olieric, N. / Standfuss, J. / Kapitein, L.C. / Lohmuller, T. / Ahlfeld, J. / Akhmanova, A. / Steinmetz, M.O. / Thorn-Seshold, O.
History
DepositionJul 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2Jan 31, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)119,5937
Polymers118,2733
Non-polymers1,3204
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-39 kcal/mol
Surface area36410 Å2
Unit cell
Length a, b, c (Å)73.900, 91.850, 82.810
Angle α, β, γ (deg.)90.000, 96.580, 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: synthetic construct (others)

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Non-polymers , 5 types, 237 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.: 1 / 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-QRQ / 2-[2-(3,4,5-trimethoxyphenyl)ethyl]-1,3-benzothiazole


Mass: 329.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19NO3S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3000, ammonium sulfate, 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 19, 2019
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→45.185 Å / Num. obs: 41022 / % possible obs: 59.5 % / Redundancy: 4.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.074 / Rrim(I) all: 0.154 / Net I/σ(I): 7.1
Reflection shellResolution: 2.04→2.327 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.124 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2024 / CC1/2: 0.951 / Rpim(I) all: 0.591 / Rrim(I) all: 1.277 / % possible all: 9.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.18refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NM5
Resolution: 2.04→45.185 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 35.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2815 1203 2.94 %
Rwork0.225 39723 -
obs0.2268 40926 58.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.85 Å2 / Biso mean: 32.8865 Å2 / Biso min: 6.62 Å2
Refinement stepCycle: final / Resolution: 2.04→45.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7853 0 84 233 8170
Biso mean--24.11 34.37 -
Num. residues----1022
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.04-2.12140.279770.32272543
2.1214-2.21790.3574230.32666769
2.2179-2.33480.3862310.325117216
2.3348-2.48110.331870.2948292539
2.4811-2.67270.36281780.2976578777
2.6727-2.94160.31342280.2795745399
2.9416-3.36710.30852220.2433737798
3.3671-4.24170.28451980.2238648086
4.2417-45.1850.20782290.1548759999

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