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Yorodumi- PDB-1x67: Solution structure of the cofilin homology domain of HIP-55 (dreb... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x67 | ||||||
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Title | Solution structure of the cofilin homology domain of HIP-55 (drebrin-like protein) | ||||||
Components | Drebrin-like protein | ||||||
Keywords | PROTEIN BINDING / cell-free protein synthesis / actin-binding protein / SH3P7 / mAbp1 / T-cell lymphocyte signaling and regulation / T-cell antigen receptor regulation / HPK-1 activation / c-JUN N-terminal kinase activation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information : / site of polarized growth / : / podosome assembly / postsynaptic actin cytoskeleton organization / ruffle assembly / positive regulation of dendritic spine morphogenesis / clathrin-coated vesicle membrane / regulation of actin filament polymerization / podosome ...: / site of polarized growth / : / podosome assembly / postsynaptic actin cytoskeleton organization / ruffle assembly / positive regulation of dendritic spine morphogenesis / clathrin-coated vesicle membrane / regulation of actin filament polymerization / podosome / Neurexins and neuroligins / cortical actin cytoskeleton / Rac protein signal transduction / Caspase-mediated cleavage of cytoskeletal proteins / positive regulation of axon extension / enzyme activator activity / synapse assembly / ruffle / neuron projection morphogenesis / receptor-mediated endocytosis / actin filament binding / tertiary granule lumen / lamellipodium / actin binding / cell cortex / postsynaptic membrane / perikaryon / secretory granule lumen / adaptive immune response / ficolin-1-rich granule lumen / postsynaptic density / early endosome / cadherin binding / protein domain specific binding / Golgi membrane / dendrite / Neutrophil degranulation / extracellular exosome / extracellular region / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Goroncy, A.K. / Kigawa, T. / Koshiba, S. / Sato, M. / Kobayashi, N. / Tochio, N. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: NMR solution structures of actin depolymerizing factor homology domains. Authors: Goroncy, A.K. / Koshiba, S. / Tochio, N. / Tomizawa, T. / Sato, M. / Inoue, M. / Watanabe, S. / Hayashizaki, Y. / Tanaka, A. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x67.cif.gz | 828.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x67.ent.gz | 700 KB | Display | PDB format |
PDBx/mmJSON format | 1x67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x67_validation.pdf.gz | 344.6 KB | Display | wwPDB validaton report |
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Full document | 1x67_full_validation.pdf.gz | 474.6 KB | Display | |
Data in XML | 1x67_validation.xml.gz | 54.9 KB | Display | |
Data in CIF | 1x67_validation.cif.gz | 65.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/1x67 ftp://data.pdbj.org/pub/pdb/validation_reports/x6/1x67 | HTTPS FTP |
-Related structure data
Related structure data | 1udmC 1v6fC 1wfsC 2d8bC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 15403.144 Da / Num. of mol.: 1 / Fragment: cofilin homology domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: CELL-FREE PROTEIN SYNTHESIS / Gene: DBNL / Plasmid: P041129-01 / References: UniProt: Q9UJU6 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.33mM COFILIN HOMOLOGY DOMAIN, 20mM TRIS-HCL, 100mM NaCl, 1mM d-DTT, 0.02% NaN3 Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |