+Open data
-Basic information
Entry | Database: PDB / ID: 7yyq | |||||||||||||||||||||
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Title | Molecular snapshots of drug release from tubulin: Dark state | |||||||||||||||||||||
Components |
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Keywords | CELL CYCLE / time-resolved serial crystallography / tubulin dynamics / azobenzene dynamics | |||||||||||||||||||||
Function / homology | Function and homology information positive regulation of axon guidance / microtubule-based process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / nervous system development / microtubule / protein heterodimerization activity ...positive regulation of axon guidance / microtubule-based process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / nervous system development / microtubule / protein heterodimerization activity / GTPase activity / GTP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | synthetic construct (others) Bos taurus (cattle) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||||||||||||||
Authors | Wranik, M. / Weinert, T. / Standfuss, J. | |||||||||||||||||||||
Funding support | Switzerland, 6items
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Citation | Journal: Nat Commun / Year: 2023 Title: Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography. Authors: Wranik, M. / Weinert, T. / Slavov, C. / Masini, T. / Furrer, A. / Gaillard, N. / Gioia, D. / Ferrarotti, M. / James, D. / Glover, H. / Carrillo, M. / Kekilli, D. / Stipp, R. / Skopintsev, P. ...Authors: Wranik, M. / Weinert, T. / Slavov, C. / Masini, T. / Furrer, A. / Gaillard, N. / Gioia, D. / Ferrarotti, M. / James, D. / Glover, H. / Carrillo, M. / Kekilli, D. / Stipp, R. / Skopintsev, P. / Brunle, S. / Muhlethaler, T. / Beale, J. / Gashi, D. / Nass, K. / Ozerov, D. / Johnson, P.J.M. / Cirelli, C. / Bacellar, C. / Braun, M. / Wang, M. / Dworkowski, F. / Milne, C. / Cavalli, A. / Wachtveitl, J. / Steinmetz, M.O. / Standfuss, J. #1: Journal: Res Sq / Year: 2022 Title: Release of a photopharmacological drug from its protein target captured by time-resolved serial crystallography Authors: Wranik, M. / Weinert, T. / Slavov, C. / Masini, T. / Furrer, A. / Gaillard, N. / Gioia, D. / Ferrarotti, M. / James, D. / Glover, H. / Carrillo, M. / Kekilli, D. / Stipp, R. / Skopintsev, P. ...Authors: Wranik, M. / Weinert, T. / Slavov, C. / Masini, T. / Furrer, A. / Gaillard, N. / Gioia, D. / Ferrarotti, M. / James, D. / Glover, H. / Carrillo, M. / Kekilli, D. / Stipp, R. / Skopintsev, P. / Brunle, S. / Muhlethaler, T. / Beale, J. / Gashi, D. / Nass, K. / Ozerov, D. / Johnson, P. / Cirelli, C. / Bacellar, C. / Braun, M. / Wang, M. / Dworkowski, F. / Milne, C. / Cavalli, A. / Wachtveitl, J. / Steinmetz, M. / Standfuss, J. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yyq.cif.gz | 631.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yyq.ent.gz | 523.9 KB | Display | PDB format |
PDBx/mmJSON format | 7yyq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yyq_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7yyq_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7yyq_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 7yyq_validation.cif.gz | 63.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/7yyq ftp://data.pdbj.org/pub/pdb/validation_reports/yy/7yyq | HTTPS FTP |
-Related structure data
Related structure data | 7yyvC 7yywC 7yyyC 7yyzC 7yz0C 7yz1C 7yz2C 7yz3C 7yz5C 7yz6C 5nqtS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: Escherichia coli BL21 (bacteria) |
-Non-polymers , 5 types, 548 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CA / | #7: Chemical | ChemComp-IBL / | #8: Water | ChemComp-HOH / | |
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-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: 2.43 Å3/Da / Density % sol: 49.45 % |
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Crystal grow | Temperature: 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) |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1 Å |
Detector | Type: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Sep 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→11.09 Å / Num. obs: 123960 / % possible obs: 100 % / Redundancy: 2089.8 % / CC1/2: 0.992 / R split: 0.075 / Net I/σ(I): 9.53 |
Reflection shell | Resolution: 1.7→1.76 Å / Mean I/σ(I) obs: 1.43 / Num. unique obs: 12356 / CC1/2: 0.694 / R split: 0.7885 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NQT Resolution: 1.7→9.49 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.66 / 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: 134.93 Å2 / Biso mean: 49.0134 Å2 / Biso min: 20.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→9.49 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
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