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Yorodumi- PDB-6nyw: Structure of spastin AAA domain N527C mutant in complex with 8-fl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nyw | |||||||||
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Title | Structure of spastin AAA domain N527C mutant in complex with 8-fluoroquinazoline-based inhibitor | |||||||||
Components | Spastin | |||||||||
Keywords | ISOMERASE/INHIBITOR / AAA+ protein / hydrolase / enzyme-INHIBITOR complex / ISOMERASE-INHIBITOR complex | |||||||||
Function / homology | Function and homology information positive regulation of axon extension involved in regeneration / hemocyte migration / negative regulation of synaptic assembly at neuromuscular junction / Sealing of the nuclear envelope (NE) by ESCRT-III / negative regulation of neuromuscular synaptic transmission / positive regulation of neuromuscular synaptic transmission / microtubule-severing ATPase / positive regulation of synaptic assembly at neuromuscular junction / microtubule severing ATPase activity / mitotic chromosome movement towards spindle pole ...positive regulation of axon extension involved in regeneration / hemocyte migration / negative regulation of synaptic assembly at neuromuscular junction / Sealing of the nuclear envelope (NE) by ESCRT-III / negative regulation of neuromuscular synaptic transmission / positive regulation of neuromuscular synaptic transmission / microtubule-severing ATPase / positive regulation of synaptic assembly at neuromuscular junction / microtubule severing ATPase activity / mitotic chromosome movement towards spindle pole / microtubule severing / regulation of terminal button organization / positive regulation of lipid metabolic process / positive regulation of microtubule depolymerization / mitotic spindle elongation / negative regulation of microtubule depolymerization / protein hexamerization / positive regulation of dendrite morphogenesis / mitotic sister chromatid segregation / alpha-tubulin binding / isomerase activity / lipid droplet / adult locomotory behavior / locomotory behavior / neuromuscular junction / terminal bouton / microtubule cytoskeleton organization / spindle / microtubule cytoskeleton / chromosome / nervous system development / microtubule binding / microtubule / cell division / centrosome / ATP hydrolysis activity / ATP binding / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.189 Å | |||||||||
Authors | Pisa, R. / Cupido, T. / Kapoor, T.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2019 Title: Designing Allele-Specific Inhibitors of Spastin, a Microtubule-Severing AAA Protein. Authors: Pisa, R. / Cupido, T. / Kapoor, T.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nyw.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nyw.ent.gz | 51.7 KB | Display | PDB format |
PDBx/mmJSON format | 6nyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nyw_validation.pdf.gz | 825.6 KB | Display | wwPDB validaton report |
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Full document | 6nyw_full_validation.pdf.gz | 828.5 KB | Display | |
Data in XML | 6nyw_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 6nyw_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/6nyw ftp://data.pdbj.org/pub/pdb/validation_reports/ny/6nyw | HTTPS FTP |
-Related structure data
Related structure data | 6nyvC 3b9pS 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 , 1 types, 1 molecules B
#1: Protein | Mass: 34310.070 Da / Num. of mol.: 1 / Mutation: N527C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: spas, CG5977 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I0P1, microtubule-severing ATPase |
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-Non-polymers , 5 types, 113 molecules
#2: Chemical | ChemComp-SO4 / | ||||
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#3: Chemical | ChemComp-L8M / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.87 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Na-acetate pH 5-6.5, 2% PEG-4000, 15% MPD / PH range: 5.5-6.5 / Temp details: 289-291 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.91806 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91806 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→50 Å / Num. obs: 17457 / % possible obs: 99.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 57.34 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.19→2.23 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 861 / CC1/2: 0.891 / Rpim(I) all: 0.228 / Rrim(I) all: 0.638 / Χ2: 0.437 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3B9P Resolution: 2.189→39.348 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 25.64 / 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: 103.1 Å2 / Biso mean: 51.763 Å2 / Biso min: 25.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.189→39.348 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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