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Yorodumi- PDB-2dmm: The solution structure of the second thioredoxin domain of human ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dmm | ||||||
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Title | The solution structure of the second thioredoxin domain of human Protein disulfide-isomerase A3 | ||||||
Components | Protein disulfide-isomerase A3 | ||||||
Keywords | ISOMERASE / Disulfide isomerase ER-60 / ERp60 / 58 kDa microsomal protein / p58 / ERp57 / 58 kDa glucose-regulated protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Tapasin-ERp57 complex / Calnexin/calreticulin cycle / protein disulfide-isomerase / protein folding in endoplasmic reticulum / disulfide oxidoreductase activity / phospholipase C activity / cellular response to interleukin-7 / positive regulation of extrinsic apoptotic signaling pathway / protein disulfide isomerase activity / protein-disulfide reductase activity ...Tapasin-ERp57 complex / Calnexin/calreticulin cycle / protein disulfide-isomerase / protein folding in endoplasmic reticulum / disulfide oxidoreductase activity / phospholipase C activity / cellular response to interleukin-7 / positive regulation of extrinsic apoptotic signaling pathway / protein disulfide isomerase activity / protein-disulfide reductase activity / phagocytic vesicle / extrinsic apoptotic signaling pathway / response to endoplasmic reticulum stress / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / platelet aggregation / recycling endosome membrane / melanosome / protein folding / ER-Phagosome pathway / adaptive immune response / endoplasmic reticulum lumen / cysteine-type endopeptidase activity / focal adhesion / cell surface / endoplasmic reticulum / extracellular space / RNA binding / extracellular exosome / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: The solution structure of the second thioredoxin domain of human Protein disulfide-isomerase A3 Authors: Tochio, N. / 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 | 2dmm.cif.gz | 840.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dmm.ent.gz | 730.1 KB | Display | PDB format |
PDBx/mmJSON format | 2dmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/2dmm ftp://data.pdbj.org/pub/pdb/validation_reports/dm/2dmm | 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: 15697.501 Da / Num. of mol.: 1 / Fragment: thioredoxin domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: PDIA3, ERP60, GRP58 / Plasmid: P050627-10 / Production host: Cell free synthesis / References: UniProt: P30101, protein disulfide-isomerase |
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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: 1.3mM thioredoxin domain U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 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: target function,structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |