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- PDB-1pn5: NMR structure of the NALP1 Pyrin domain (PYD) -

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Basic information

Entry
Database: PDB / ID: 1pn5
TitleNMR structure of the NALP1 Pyrin domain (PYD)
ComponentsNACHT-, LRR- and PYD-containing protein 2
KeywordsAPOPTOSIS / 5 ALPHA-HELIX BUNDLE
Function / homology
Function and homology information


NLRP1 inflammasome complex assembly / NLRP1 inflammasome complex / The NLRP1 inflammasome / NLRP3 inflammasome complex / self proteolysis / cysteine-type endopeptidase activator activity / Hydrolases; Acting on peptide bonds (peptidases) / IgG binding / pattern recognition receptor signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process ...NLRP1 inflammasome complex assembly / NLRP1 inflammasome complex / The NLRP1 inflammasome / NLRP3 inflammasome complex / self proteolysis / cysteine-type endopeptidase activator activity / Hydrolases; Acting on peptide bonds (peptidases) / IgG binding / pattern recognition receptor signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process / cellular response to UV-B / pattern recognition receptor activity / pyroptotic inflammatory response / response to muramyl dipeptide / signaling adaptor activity / antiviral innate immune response / activation of innate immune response / intrinsic apoptotic signaling pathway / positive regulation of interleukin-1 beta production / molecular condensate scaffold activity / protein homooligomerization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / positive regulation of inflammatory response / peptidase activity / double-stranded RNA binding / double-stranded DNA binding / regulation of inflammatory response / neuron apoptotic process / regulation of apoptotic process / defense response to virus / defense response to bacterium / inflammatory response / protein domain specific binding / apoptotic process / nucleolus / enzyme binding / signal transduction / ATP hydrolysis activity / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
FIIND domain / Function to find / UPA-FIIND domain / FIIND domain profile. / CARD8/ASC/NALP1, CARD domain / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain ...FIIND domain / Function to find / UPA-FIIND domain / FIIND domain profile. / CARD8/ASC/NALP1, CARD domain / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / 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 / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Leucine rich repeat, ribonuclease inhibitor type / Immunoglobulin/albumin-binding domain superfamily / Leucine Rich repeat / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Leucine Rich Repeat / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Death-like domain superfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Immunoglobulin G-binding protein G / NACHT, LRR and PYD domains-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHiller, S. / Kohl, A. / Fiorito, F. / Herrmann, T. / Wider, G. / Tschopp, J. / Grutter, M.G. / Wuthrich, K.
CitationJournal: Structure / Year: 2003
Title: NMR structure of the apoptosis- and inflammation-related NALP1 pyrin domain
Authors: Hiller, S. / Kohl, A. / Fiorito, F. / Herrmann, T. / Wider, G. / Tschopp, J. / Grutter, M.G. / Wuthrich, K.
History
DepositionJun 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE Residues 1-58 are missing from the coordinates because they were not included in the model. ...SEQUENCE Residues 1-58 are missing from the coordinates because they were not included in the model. Residues 57 and 58 are independent linking residues, which have been inserted to provide distance and flexibiltiy in this two-domain fusion protein.
Remark 650HELIX Determination method: author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NACHT-, LRR- and PYD-containing protein 2


Theoretical massNumber of molelcules
Total (without water)17,6811
Polymers17,6811
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #17aesthetic reasons

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Components

#1: Protein NACHT-, LRR- and PYD-containing protein 2 / Death effector filament-forming ced-4-like apoptosis protein / Nucleotide-binding domain and ...Death effector filament-forming ced-4-like apoptosis protein / Nucleotide-binding domain and caspase recruitment domain / Caspase recruitment domain protein 7


Mass: 17680.607 Da / Num. of mol.: 1 / Fragment: Pyrin domain (PYD)
Source method: isolated from a genetically manipulated source
Details: Residues 1-56 correspond to the fused Immunoglobulin G binding protein G (SWS P06654, residues 228-282)
Source: (gene. exp.) Homo sapiens (human) / Gene: NALP1 / Plasmid: pET20b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P06654, UniProt: Q9C000

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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
NMR detailsText: Protein was expressed as a fusion protein with G B1 to enhance solubility (Zhou et al., J. Biomol. NMR 20, 11-14)

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Sample preparation

DetailsContents: 1mM NALP1 PYD U-15N,13C; 50mM Na / PO4 - Buffer; 50mM NaCl; 1mM CHAPS; 20mM DTT (D10); 0.02% NaN3; 0.1mM EDTA; protease inhibitor cocktail (Complete, Roche); 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionspH: 6.5 / Pressure: 1 atm / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX7501
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameDeveloperClassification
XwinNMRBrukercollection
DYANAGuentertstructure solution
CANDIDHerrmannstructure solution
ATNOSHerrmannstructure solution
CARAKellerdata analysis
ATNOSHerrmannrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: aesthetic reasons
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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