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Yorodumi- PDB-2do9: Solution structure of the Pyrin/PAAD-DAPIN domain in mouse NALP10... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2do9 | ||||||
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Title | Solution structure of the Pyrin/PAAD-DAPIN domain in mouse NALP10 (NACHT, leucine rich repeat and PYD containing 10) | ||||||
Components | NACHT-, LRR- and PYD-containing protein 10 | ||||||
Keywords | SIGNALING PROTEIN / NALP / apoptosis / inflammation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information positive regulation of defense response to bacterium / positive regulation of interleukin-1 alpha production / positive regulation of T-helper 1 type immune response / positive regulation of T-helper 17 type immune response / extrinsic component of plasma membrane / defense response to fungus / positive regulation of interleukin-8 production / positive regulation of inflammatory response / positive regulation of interleukin-6 production / defense response to Gram-negative bacterium ...positive regulation of defense response to bacterium / positive regulation of interleukin-1 alpha production / positive regulation of T-helper 1 type immune response / positive regulation of T-helper 17 type immune response / extrinsic component of plasma membrane / defense response to fungus / positive regulation of interleukin-8 production / positive regulation of inflammatory response / positive regulation of interleukin-6 production / defense response to Gram-negative bacterium / adaptive immune response / inflammatory response / innate immune response / GTPase activity / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | 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 Pyrin/PAAD-DAPIN domain in mouse NALP10 (NACHT, leucine rich repeat and PYD containing 10) Authors: 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 | 2do9.cif.gz | 688.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2do9.ent.gz | 576.4 KB | Display | PDB format |
PDBx/mmJSON format | 2do9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2do9_validation.pdf.gz | 343.8 KB | Display | wwPDB validaton report |
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Full document | 2do9_full_validation.pdf.gz | 478.8 KB | Display | |
Data in XML | 2do9_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 2do9_validation.cif.gz | 54 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/2do9 ftp://data.pdbj.org/pub/pdb/validation_reports/do/2do9 | 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: 12760.375 Da / Num. of mol.: 1 / Fragment: PYD domain, DAPIN domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: cell-free protein synthesis / Gene: 4732403D13, Nalp10, Pynod / Plasmid: P050912-07 / Production host: Cell free synthesis / References: UniProt: Q8CCN1 |
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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: 1mM protein; 20mM d-Tris-HCL(pH 7.0); 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: 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: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |