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Yorodumi- PDB-1wx9: Solution Structure of the N-terminal Ubiquitin-like Domain in the... -
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-Basic information
Entry | Database: PDB / ID: 1wx9 | ||||||
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Title | Solution Structure of the N-terminal Ubiquitin-like Domain in the Human BAT3 Protein | ||||||
Components | HLA-B associated transcript-3 isoform b | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / ubiquitin-like domain / BAT3 protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information maintenance of unfolded protein involved in ERAD pathway / : / : / BAT3 complex / immune response-activating cell surface receptor signaling pathway / maintenance of unfolded protein / : / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / synaptonemal complex assembly ...maintenance of unfolded protein involved in ERAD pathway / : / : / BAT3 complex / immune response-activating cell surface receptor signaling pathway / maintenance of unfolded protein / : / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / synaptonemal complex assembly / post-translational protein targeting to endoplasmic reticulum membrane / internal peptidyl-lysine acetylation / misfolded protein binding / natural killer cell activation / endoplasmic reticulum stress-induced pre-emptive quality control / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / proteasome binding / ubiquitin-specific protease binding / regulation of embryonic development / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / ERAD pathway / Hsp70 protein binding / kidney development / molecular function activator activity / negative regulation of proteolysis / lung development / regulation of protein stability / brain development / ribosome binding / chromatin organization / regulation of cell population proliferation / ubiquitin-dependent protein catabolic process / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / molecular adaptor activity / cell differentiation / protein stabilization / intracellular membrane-bounded organelle / signaling receptor binding / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Zhao, C. / 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 the N-terminal Ubiquitin-like Domain in the Human BAT3 Protein Authors: Zhao, C. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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Remark 650 | HELIX Determination method: Author determined | ||||||
Remark 700 | SHEET Determination method: Author determined |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wx9.cif.gz | 510.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wx9.ent.gz | 427.4 KB | Display | PDB format |
PDBx/mmJSON format | 1wx9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wx9_validation.pdf.gz | 344.2 KB | Display | wwPDB validaton report |
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Full document | 1wx9_full_validation.pdf.gz | 484.2 KB | Display | |
Data in XML | 1wx9_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 1wx9_validation.cif.gz | 51.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/1wx9 ftp://data.pdbj.org/pub/pdb/validation_reports/wx/1wx9 | HTTPS FTP |
-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: 9296.517 Da / Num. of mol.: 1 / Fragment: ubiquitin-like domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: BAT3 / Plasmid: P040921-06 / References: UniProt: Q5STX1, UniProt: P46379*PLUS |
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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: 1.23mM protein 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: 100mM / pH: 7.0 / Pressure: ambient / Temperature: 298.0 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
-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 |