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Yorodumi- PDB-2d9d: Solution structure of the BAG domain (275-350) of BAG-family mole... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d9d | ||||||
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Title | Solution structure of the BAG domain (275-350) of BAG-family molecular chaperone regulator-5 | ||||||
Components | BAG family molecular chaperone regulator 5 | ||||||
Keywords | CHAPERONE / triple helix bundle / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information regulation of inclusion body assembly / junctional membrane complex / negative regulation of protein refolding / regulation of ubiquitin-protein transferase activity / adenyl-nucleotide exchange factor activity / negative regulation of ubiquitin-protein transferase activity / Golgi organization / Regulation of HSF1-mediated heat shock response / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / inclusion body ...regulation of inclusion body assembly / junctional membrane complex / negative regulation of protein refolding / regulation of ubiquitin-protein transferase activity / adenyl-nucleotide exchange factor activity / negative regulation of ubiquitin-protein transferase activity / Golgi organization / Regulation of HSF1-mediated heat shock response / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / inclusion body / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / negative regulation of neuron projection development / protein folding / protein-folding chaperone binding / protein stabilization / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / mitochondrion / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Hatta, R. / Hayashi, F. / Yoshida, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Structure / Year: 2010 Title: The C-terminal BAG domain of BAG5 induces conformational changes of the Hsp70 nucleotide-binding domain for ADP-ATP exchange Authors: Arakawa, A. / Handa, N. / Ohsawa, N. / Shida, M. / Kigawa, T. / Hayashi, F. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d9d.cif.gz | 544.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d9d.ent.gz | 458 KB | Display | PDB format |
PDBx/mmJSON format | 2d9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/2d9d ftp://data.pdbj.org/pub/pdb/validation_reports/d9/2d9d | HTTPS FTP |
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-Related structure data
Related structure data | 1ugoC 1uk5C 3a8yC 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: 9842.250 Da / Num. of mol.: 1 / Fragment: BAG domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAG5 / Plasmid: P04070-E03 / Production host: cell free protein synthesis (others) / References: UniProt: Q9UL15 |
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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: 0.96mM 13C, 15N-labeled protein; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 75mM GuOx; 90% H2O; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 345mM / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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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: target function, structures with the lowest energy, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |