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Yorodumi- PDB-1p8z: Complex Between Rabbit Muscle alpha-Actin: Human Gelsolin Residue... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p8z | ||||||
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Title | Complex Between Rabbit Muscle alpha-Actin: Human Gelsolin Residues Val26-Glu156 | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/CONTRACTILE PROTEIN / linker between Gelsolin Domain 1 and Domain 2 / STRUCTURAL PROTEIN-CONTRACTILE PROTEIN COMPLEX | ||||||
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 cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding ...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 cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / actin cap / regulation of podosome assembly / sequestering of actin monomers / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / barbed-end actin filament capping / cell projection assembly / cardiac muscle cell contraction / podosome / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / cytoskeletal motor activator activity / cortical actin cytoskeleton / phagocytosis, engulfment / tropomyosin binding / mesenchyme migration / hepatocyte apoptotic process / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / sarcoplasm / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / skeletal muscle fiber development / stress fiber / titin binding / phagocytic vesicle / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / filopodium / central nervous system development / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein destabilization / cellular response to type II interferon / actin filament binding / calcium-dependent protein binding / actin cytoskeleton / lamellipodium / actin binding / cell body / secretory granule lumen / ficolin-1-rich granule lumen / amyloid fibril formation / blood microparticle / hydrolase activity / protein domain specific binding / Amyloid fiber formation / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / magnesium ion binding / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Irobi, E. / Burtnick, L.D. / Robinson, R.C. | ||||||
Citation | Journal: FEBS lett. / Year: 2003 Title: From the First to the second domain of gelsolin: A common path on the surface of actin? Authors: Irobi, E. / Burtnick, L.D. / Urosev, D. / Narayan, K. / Robinson, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p8z.cif.gz | 116.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p8z.ent.gz | 87.3 KB | Display | PDB format |
PDBx/mmJSON format | 1p8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p8z_validation.pdf.gz | 759.6 KB | Display | wwPDB validaton report |
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Full document | 1p8z_full_validation.pdf.gz | 775.8 KB | Display | |
Data in XML | 1p8z_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 1p8z_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/1p8z ftp://data.pdbj.org/pub/pdb/validation_reports/p8/1p8z | HTTPS FTP |
-Related structure data
Similar structure data |
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-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
-Protein , 2 types, 2 molecules GA
#1: Protein | Mass: 15303.274 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P06396 |
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#2: Protein | Mass: 42096.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135 |
-Non-polymers , 4 types, 189 molecules
#3: Chemical | #4: Chemical | ChemComp-CA / | #5: Chemical | ChemComp-ATP / | #6: 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: 3.07 Å3/Da / Density % sol: 60 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1M Sodium Acetate, 10 mM Cadmium Chloride, 12.5% (v/v) PEG 400, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0052 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 7, 2003 |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0052 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 21012 / Num. obs: 21012 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.6→2.69 Å / % possible all: 99.2 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.077 |
Reflection shell | *PLUS % possible obs: 99.2 % / Redundancy: 3.9 % / Num. unique obs: 2115 / Rmerge(I) obs: 0.267 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.69 Å
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.6 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS |