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Yorodumi- PDB-6qbf: Crystal structure of the pathological D187N variant of calcium-fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qbf | ||||||
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Title | Crystal structure of the pathological D187N variant of calcium-free human gelsolin. | ||||||
Components | Gelsolin | ||||||
Keywords | STRUCTURAL PROTEIN / amyloidosis / gelsolin / actin-binding / pathological mutation | ||||||
Function / homology | Function and homology information striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway ...striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / actin cap / sequestering of actin monomers / regulation of podosome assembly / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / actin filament capping / barbed-end actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / cell projection assembly / cardiac muscle cell contraction / podosome / sarcoplasm / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / phagocytosis, engulfment / cortical actin cytoskeleton / hepatocyte apoptotic process / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / central nervous system development / actin filament organization / protein destabilization / cellular response to type II interferon / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / blood microparticle / secretory granule lumen / ficolin-1-rich granule lumen / amyloid fibril formation / Amyloid fiber formation / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.499 Å | ||||||
Authors | Scalone, E. / Boni, F. / Milani, M. / Eloise, M. / de Rosa, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Eur.Biophys.J. / Year: 2020 Title: The structure of N184K amyloidogenic variant of gelsolin highlights the role of the H-bond network for protein stability and aggregation properties. Authors: de Rosa, M. / Barbiroli, A. / Boni, F. / Scalone, E. / Mattioni, D. / Vanoni, M.A. / Patrone, M. / Bollati, M. / Mastrangelo, E. / Giorgino, T. / Milani, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qbf.cif.gz | 567.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qbf.ent.gz | 468.8 KB | Display | PDB format |
PDBx/mmJSON format | 6qbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/6qbf ftp://data.pdbj.org/pub/pdb/validation_reports/qb/6qbf | HTTPS FTP |
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-Related structure data
Related structure data | 6q9rC 6q9zC 3ffnS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 85516.703 Da / Num. of mol.: 2 / Mutation: D187N Source method: isolated from a genetically manipulated source Details: D187N (p.D214N) / Source: (gene. exp.) Homo sapiens (human) / Gene: GSN / Production host: Escherichia coli (E. coli) / References: UniProt: P06396 #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
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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: 3.45 Å3/Da / Density % sol: 64.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.3 M Ammonium sulfate, 19% glycerol, 100 mM Tris HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.992 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.992 Å / Relative weight: 1 |
Reflection | Resolution: 3.499→84.98 Å / Num. obs: 28491 / % possible obs: 99.5 % / Redundancy: 10.3 % / CC1/2: 0.948 / Rrim(I) all: 0.482 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 3.499→3.69 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2 / CC1/2: 0.265 / Rrim(I) all: 0.971 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FFN Resolution: 3.499→75.88 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.66 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.499→75.88 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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