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Yorodumi- PDB-2eno: Solution structure of the PDZ domain from human Synaptojanin 2 bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2eno | ||||||
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Title | Solution structure of the PDZ domain from human Synaptojanin 2 binding protein | ||||||
Components | Synaptojanin-2-binding protein | ||||||
Keywords | ENDOCYTOSIS / Mitochondrial outer membrane protein 25 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information negative regulation of sprouting angiogenesis / embryo development / regulation of Notch signaling pathway / receptor localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of endothelial cell migration / receptor clustering / negative regulation of endothelial cell proliferation / Rho protein signal transduction / regulation of endocytosis ...negative regulation of sprouting angiogenesis / embryo development / regulation of Notch signaling pathway / receptor localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of endothelial cell migration / receptor clustering / negative regulation of endothelial cell proliferation / Rho protein signal transduction / regulation of endocytosis / protein targeting / negative regulation of angiogenesis / postsynaptic density membrane / neuromuscular junction / negative regulation of ERK1 and ERK2 cascade / cell-cell adhesion / chemical synaptic transmission / basolateral plasma membrane / mitochondrial outer membrane / neuron projection / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Endo, H. / Yoshida, M. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the PDZ domain from human Synaptojanin 2 binding protein Authors: Endo, H. / Yoshida, M. / Hayashi, F. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2eno.cif.gz | 682.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eno.ent.gz | 571.5 KB | Display | PDB format |
PDBx/mmJSON format | 2eno.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/2eno ftp://data.pdbj.org/pub/pdb/validation_reports/en/2eno | HTTPS FTP |
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-Related structure data
Similar structure data | |
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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: 12686.882 Da / Num. of mol.: 1 / Fragment: PDZ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: SYNJ2BP / Plasmid: P050509-14 / References: UniProt: P57105 |
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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: 1.22mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH 7.0), 100mM NaCl; 1mM d-DTT; 0.02% NaN3, 10% D2O; 90% H2O Solvent system: 10% D2O; 90% H2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |