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Yorodumi- PDB-2ctt: Solution structure of zinc finger domain from human DnaJ subfamil... -
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-Basic information
Entry | Database: PDB / ID: 2ctt | ||||||
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Title | Solution structure of zinc finger domain from human DnaJ subfamily A menber 3 | ||||||
Components | DnaJ homolog subfamily A member 3 | ||||||
Keywords | CHAPERONE / DnaJ / Zing finger / beta-hairpin / 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 / activation-induced cell death of T cells / GTPase regulator activity / mitochondrial DNA replication / small GTPase-mediated signal transduction / neuromuscular junction development / negative regulation of NF-kappaB transcription factor activity / negative regulation of type II interferon-mediated signaling pathway ...IkappaB kinase complex binding / type II interferon receptor binding / skeletal muscle acetylcholine-gated channel clustering / activation-induced cell death of T cells / GTPase regulator activity / mitochondrial DNA replication / small GTPase-mediated signal transduction / neuromuscular junction development / negative regulation of NF-kappaB transcription factor activity / negative regulation of type II interferon-mediated signaling pathway / response to type II interferon / mitochondrial nucleoid / NF-kappaB binding / negative regulation of canonical NF-kappaB signal transduction / Hsp70 protein binding / positive regulation of T cell proliferation / mitochondrion organization / positive regulation of protein ubiquitination / negative regulation of protein kinase activity / neuromuscular junction / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / Tosion angle dynamics | ||||||
Authors | Kobayashi, N. / Tochio, N. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of zinc finger domain from human DnaJ subfamily A menber 3 Authors: Kobayashi, N. / Tochio, N. / Saito, K. / 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 | 2ctt.cif.gz | 577.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ctt.ent.gz | 501.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ctt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/2ctt ftp://data.pdbj.org/pub/pdb/validation_reports/ct/2ctt | 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: 10850.353 Da / Num. of mol.: 1 / Fragment: Zinc finger domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: DNAJA3 / Plasmid: P040628-14 / References: UniProt: Q96EY1 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.08mM Zinc finger domain U-13C,15N; 20mM Phosphate buffer Na (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.01mM ZnCl2; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 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: Tosion 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 |