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- PDB-7yyx: Molecular snapshots of drug release from tubulin: 100 nanoseconds... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yyx | |||||||||||||||||||||
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Title | Molecular snapshots of drug release from tubulin: 100 nanoseconds after photoactivation. | |||||||||||||||||||||
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![]() | CELL CYCLE / time-resolved serial crystallography / tubulin dynamics / azobenzene dynamics | |||||||||||||||||||||
Function / homology | ![]() 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)![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Wranik, M. / Weinert, T. / Standfuss, J. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 220.9 KB | Display | ![]() |
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PDB format | ![]() | 169.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7yyqC ![]() 7yyvC ![]() 7yywC ![]() 7yyyC ![]() 7yyzC ![]() 7yz0C ![]() 7yz1C ![]() 7yz2C ![]() 7yz3C ![]() 7yz5C ![]() 7yz6C ![]() 5nqtS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() Data set type: diffraction image data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() ![]() |
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#2: Protein | Mass: 49999.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#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: ![]() ![]() |
-Non-polymers , 6 types, 216 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/VYT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/VYT.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GTP / |
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#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-CA / |
#7: Chemical | ChemComp-GDP / |
#8: Chemical | ChemComp-VYT / |
#9: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() |
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: 122150 / % possible obs: 100 % / Redundancy: 314.1 % / CC1/2: 0.964 / R split: 0.181 / Net I/σ(I): 4.05 |
Reflection shell | Resolution: 1.7→1.76 Å / Mean I/σ(I) obs: 0.62 / Num. unique obs: 12154 / CC1/2: 0.323 / R split: 1.804 |
Serial crystallography sample delivery | Method: injection |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 5NQT Resolution: 2.2→9.49 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 41.08 / 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: 80.14 Å2 / Biso mean: 34.6528 Å2 / Biso min: 14.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→9.49 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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