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Yorodumi- PDB-2k8a: Solution structure of a novel Ubiquitin-binding domain from Human... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2k8a | ||||||
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Title | Solution structure of a novel Ubiquitin-binding domain from Human PLAA (PFUC, Gly76-Pro77 trans isomer) | ||||||
Components | Phospholipase A-2-activating protein | ||||||
Keywords | PROTEIN BINDING / Ubiquitin binding / WD repeat | ||||||
Function / homology | Function and homology information positive regulation of synaptic vesicle recycling / negative regulation of protein K63-linked ubiquitination / positive regulation of phospholipase A2 activity / ubiquitin recycling / positive regulation of neuron migration / phospholipase A2 activator activity / positive regulation of dendrite extension / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / prostaglandin metabolic process / phospholipid metabolic process ...positive regulation of synaptic vesicle recycling / negative regulation of protein K63-linked ubiquitination / positive regulation of phospholipase A2 activity / ubiquitin recycling / positive regulation of neuron migration / phospholipase A2 activator activity / positive regulation of dendrite extension / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / prostaglandin metabolic process / phospholipid metabolic process / ubiquitin binding / macroautophagy / nervous system development / cellular response to lipopolysaccharide / proteasome-mediated ubiquitin-dependent protein catabolic process / inflammatory response / synapse / signal transduction / extracellular exosome / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Fu, Q.S. / Zhou, C.J. / Gao, H.C. / Lin, D.H. / Hu, H.Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structural Basis for Ubiquitin Recognition by a Novel Domain from Human Phospholipase A2-activating Protein. Authors: Fu, Q.S. / Zhou, C.J. / Gao, H.C. / Jiang, Y.J. / Zhou, Z.R. / Hong, J. / Yao, W.M. / Song, A.X. / Lin, D.H. / Hu, H.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2k8a.cif.gz | 403.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2k8a.ent.gz | 341.7 KB | Display | PDB format |
PDBx/mmJSON format | 2k8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2k8a_validation.pdf.gz | 345.8 KB | Display | wwPDB validaton report |
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Full document | 2k8a_full_validation.pdf.gz | 445.3 KB | Display | |
Data in XML | 2k8a_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 2k8a_validation.cif.gz | 36.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/2k8a ftp://data.pdbj.org/pub/pdb/validation_reports/k8/2k8a | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9032.011 Da / Num. of mol.: 1 / Fragment: UNP residues 386-465 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLAA, PLAP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y263 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 50mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz |
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-Processing
NMR software | Name: CNS / Developer: Brunger, Adams, Clore, Gros, Nilges and Read / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: The structures were calculated with aria/cns using torsion angle dynamics |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: 15 structures for lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 15 |