+Open data
-Basic information
Entry | Database: PDB / ID: 6zwc | ||||||
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Title | Z-SBTub2 photoswitch bound to tubulin-DARPin D1 complex | ||||||
Components |
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Keywords | CELL 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 | ||||||
Biological species | synthetic construct (others) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Wranik, 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. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zwc.cif.gz | 221 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zwc.ent.gz | 170.4 KB | Display | PDB format |
PDBx/mmJSON format | 6zwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/6zwc ftp://data.pdbj.org/pub/pdb/validation_reports/zw/6zwc | HTTPS FTP |
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-Related structure data
Related structure data | 6zwbC 5nm5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 3 types, 3 molecules ABF
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P81947 |
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#2: Protein | 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 | 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) |
-Non-polymers , 5 types, 237 molecules
#4: Chemical | ChemComp-GTP / |
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#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-GDP / |
#7: Chemical | ChemComp-QRQ / |
#8: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3000, ammonium sulfate, bis-tris methane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2019 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.85 Å2 / Biso mean: 32.8865 Å2 / Biso min: 6.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.04→45.185 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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