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Yorodumi- PDB-6p13: Structure of spastin AAA domain (T692A mutant) in complex with a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p13 | |||||||||
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Title | Structure of spastin AAA domain (T692A mutant) in complex with a diaminotriazole-based inhibitor (crystal form A) | |||||||||
Components | Spastin | |||||||||
Keywords | ISOMERASE/ISOMERASE INHIBITOR / inhibitor / complex / AAA protein / ISOMERASE-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: 2.1 Å | |||||||||
Authors | Pisa, R. / Cupido, T. / Kapoor, T.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell Chem Biol / Year: 2019 Title: Analyzing Resistance to Design Selective Chemical Inhibitors for AAA Proteins. Authors: Pisa, R. / Cupido, T. / Steinman, J.B. / Jones, N.H. / 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 | 6p13.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p13.ent.gz | 51.5 KB | Display | PDB format |
PDBx/mmJSON format | 6p13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p13_validation.pdf.gz | 724 KB | Display | wwPDB validaton report |
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Full document | 6p13_full_validation.pdf.gz | 726.6 KB | Display | |
Data in XML | 6p13_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 6p13_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/6p13 ftp://data.pdbj.org/pub/pdb/validation_reports/p1/6p13 | HTTPS FTP |
-Related structure data
Related structure data | 6p10C 6p11C 6p12C 6p14C 3b9pS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 34291.004 Da / Num. of mol.: 1 / Fragment: AAA domain (UNP residues 445-758) / Mutation: T692A 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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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-NKY / |
#4: Chemical | ChemComp-MPD / ( |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.26 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium acetate, pH 5.0-6.5, 2% PEG4000, 15% MPD PH range: 5.0-6.5 |
-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: 0.9201 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 28, 2018 |
Diffraction measurement | Details: 1.00 degrees, 0.20 sec, detector distance 220.00 mm Method: \w scans |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.052 / Number: 400597 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 20423 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 46.0316109984 Å2 / Rmerge(I) obs: 0.043 / Net I/av σ(I): 42 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 6 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1015 / CC1/2: 0.869 / % possible all: 100 |
Cell measurement | Reflection used: 400597 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3B9P Resolution: 2.1→39.849 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.79 Å2 / Biso mean: 50.7305 Å2 / Biso min: 27.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→39.849 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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