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Yorodumi- PDB-2dn9: Solution structure of J-domain from the DnaJ homolog, human Tid1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dn9 | ||||||
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Title | Solution structure of J-domain from the DnaJ homolog, human Tid1 protein | ||||||
Components | DnaJ homolog subfamily A member 3 | ||||||
Keywords | APOPTOSIS / CHAPERONE / DnaJ / J-domain / Tid1 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information IkappaB kinase complex binding / type II interferon receptor binding / skeletal muscle acetylcholine-gated channel clustering / GTPase regulator activity / mitochondrial DNA replication / negative regulation of NF-kappaB transcription factor activity / neuromuscular junction development / small GTPase-mediated signal transduction / activation-induced cell death of T cells / negative regulation of type II interferon-mediated signaling pathway ...IkappaB kinase complex binding / type II interferon receptor binding / skeletal muscle acetylcholine-gated channel clustering / GTPase regulator activity / mitochondrial DNA replication / negative regulation of NF-kappaB transcription factor activity / neuromuscular junction development / small GTPase-mediated signal transduction / activation-induced cell death of T cells / negative regulation of type II interferon-mediated signaling pathway / response to type II interferon / mitochondrial nucleoid / NF-kappaB binding / positive regulation of T cell proliferation / negative regulation of canonical NF-kappaB signal transduction / Hsp70 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / mitochondrion organization / positive regulation of protein ubiquitination / negative regulation of protein kinase activity / neuromuscular junction / cytoplasmic side of plasma membrane / activation of cysteine-type endopeptidase activity involved in apoptotic process / cellular senescence / unfolded protein binding / protein folding / T cell differentiation in thymus / response to heat / postsynaptic membrane / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / protein stabilization / mitochondrial matrix / positive regulation of apoptotic process / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, restrained molecular dynamics | ||||||
Authors | Kobayashi, N. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of J-domain from the DnaJ homolog, human Tid1 protein Authors: Kobayashi, N. / Tomizawa, T. / Koshiba, S. / Inoue, M. / 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 | 2dn9.cif.gz | 468.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dn9.ent.gz | 394.6 KB | Display | PDB format |
PDBx/mmJSON format | 2dn9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/2dn9 ftp://data.pdbj.org/pub/pdb/validation_reports/dn/2dn9 | 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: 8782.624 Da / Num. of mol.: 1 / Fragment: J-domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free synthesis / Gene: DNAJA3 / Plasmid: P050516-13 / Production host: Cell free synthesis / References: UniProt: Q96EY1 |
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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: 1.06mM J-domain U-13C, 15N; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, restrained molecular dynamics Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |