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- PDB-2hm2: Solution structure of ASC2 -

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Basic information

Entry
Database: PDB / ID: 2hm2
TitleSolution structure of ASC2
ComponentsPyrin-only protein 1
KeywordsAPOPTOSIS / pyrin domain / six helix bundle
Function / homology
Function and homology information


IkappaB kinase complex / negative regulation of NF-kappaB transcription factor activity / negative regulation of tumor necrosis factor-mediated signaling pathway / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-1 beta production / negative regulation of protein kinase activity / innate immune response / nucleus / cytosol
Similarity search - Function
DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / Death Domain, Fas / PAAD/DAPIN/Pyrin domain / Death Domain, Fas / Death-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Pyrin domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsNatarajan, A. / Ghose, R. / Hill, J.M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure and dynamics of ASC2, a pyrin domain-only protein that regulates inflammatory signaling
Authors: Natarajan, A. / Ghose, R. / Hill, J.M.
History
DepositionJul 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
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
Q: Pyrin-only protein 1


Theoretical massNumber of molelcules
Total (without water)10,1221
Polymers10,1221
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 / 50structures with the least restraint violations,structures with the lowest energy
Representative

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Components

#1: Protein Pyrin-only protein 1 / ASC2 / Pyrin domain containing 1 / PAAD-only protein


Mass: 10121.882 Da / Num. of mol.: 1 / Fragment: pyrin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POP1, PYDC1 / Plasmid: pQE-30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8WXC3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: Various double and triple resonance experiments

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Sample preparation

DetailsContents: 1 mM ASC2 U-15N,13C / Solvent system: H2O/D2O (9:1) or D2O
Sample conditionsIonic strength: 10 mM sodium phosphate and 140 mM NaCl / pH: 7.3 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR softwareName: XPLOR-NIH / Version: 2.11.2 / Developer: Schwieters, Kuszewski, Tjandra, Clore / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1778 NMR-derived restraints, including 1338 NOEs, 197 dihedral angle restraints, 73 3J(NH-HA) coupling constants and 170 13CA/CB secondary shift restraints
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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