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- PDB-2do9: Solution structure of the Pyrin/PAAD-DAPIN domain in mouse NALP10... -

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Entry
Database: PDB / ID: 2do9
TitleSolution structure of the Pyrin/PAAD-DAPIN domain in mouse NALP10 (NACHT, leucine rich repeat and PYD containing 10)
ComponentsNACHT-, LRR- and PYD-containing protein 10
KeywordsSIGNALING 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 / defense response to fungus / activation of innate immune response / positive regulation of interleukin-8 production / positive regulation of interleukin-6 production / cytoplasmic side of plasma membrane / positive regulation of inflammatory response ...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 / defense response to fungus / activation of innate immune response / positive regulation of interleukin-8 production / positive regulation of interleukin-6 production / cytoplasmic side of plasma membrane / positive regulation of inflammatory response / nuclear membrane / adaptive immune response / inflammatory response / innate immune response / GTPase activity / ATP hydrolysis activity / nucleoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
: / NOD2, winged helix domain / NOD2 winged helix domain / DAPIN domain / NACHT nucleoside triphosphatase / NACHT domain / DAPIN domain profile. / NACHT-NTPase domain profile. / PAAD/DAPIN/Pyrin domain / Death Domain, Fas ...: / NOD2, winged helix domain / NOD2 winged helix domain / DAPIN domain / NACHT nucleoside triphosphatase / NACHT domain / DAPIN domain profile. / NACHT-NTPase domain profile. / PAAD/DAPIN/Pyrin domain / Death Domain, Fas / PAAD/DAPIN/Pyrin domain / Death Domain, Fas / Death-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NACHT, LRR and PYD domains-containing protein 10
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsSaito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: 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
DepositionApr 28, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NACHT-, LRR- and PYD-containing protein 10


Theoretical massNumber of molelcules
Total (without water)12,7601
Polymers12,7601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein NACHT-, LRR- and PYD-containing protein 10 / NALP10


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 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
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6brukercollection
NMRPipe2002Delaglio, F.processing
NMRView5Johnson, B.A.data analysis
CNS1.1structure solution
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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