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- PDB-2km6: NMR structure of the NLRP7 Pyrin domain -

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Basic information

Entry
Database: PDB / ID: 2km6
TitleNMR structure of the NLRP7 Pyrin domain
ComponentsNACHT, LRR and PYD domains-containing protein 7
KeywordsSIGNALING PROTEIN / PROTEIN BINDING / NLRP7 / pyrin domain / innate immune system / NALP / ATP-binding / Disease mutation / Leucine-rich repeat / Nucleotide-binding / IMMUNE SYSTEM
Function / homology
Function and homology information


negative regulation of aspartic-type peptidase activity / interleukin-1 binding / caspase binding / aspartic-type endopeptidase inhibitor activity / negative regulation of protein processing / negative regulation of interleukin-1 beta production / negative regulation of cytokine production involved in inflammatory response / cellular response to interleukin-1 / positive regulation of interleukin-1 beta production / cellular response to lipopolysaccharide ...negative regulation of aspartic-type peptidase activity / interleukin-1 binding / caspase binding / aspartic-type endopeptidase inhibitor activity / negative regulation of protein processing / negative regulation of interleukin-1 beta production / negative regulation of cytokine production involved in inflammatory response / cellular response to interleukin-1 / positive regulation of interleukin-1 beta production / cellular response to lipopolysaccharide / ATP binding / identical protein binding
Similarity search - Function
NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / Death Domain, Fas / NACHT nucleoside triphosphatase / NACHT 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 / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / Death Domain, Fas / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / PAAD/DAPIN/Pyrin domain / Death Domain, Fas / Death-like domain superfamily / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NACHT, LRR and PYD domains-containing protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsPinheiro, A. / Proell, M. / Schwarzenbacher, R. / Peti, W.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Three-dimensional structure of the NLRP7 pyrin domain: insight into pyrin-pyrin-mediated effector domain signaling in innate immunity.
Authors: Pinheiro, A.S. / Proell, M. / Eibl, C. / Page, R. / Schwarzenbacher, R. / Peti, W.
History
DepositionJul 21, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NACHT, LRR and PYD domains-containing protein 7


Theoretical massNumber of molelcules
Total (without water)12,3621
Polymers12,3621
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 domains-containing protein 7 / PYRIN-containing APAF1-like protein 3 / Nucleotide-binding oligomerization domain protein 12


Mass: 12361.915 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLRP7, NALP7, NOD12, PYPAF3 / Plasmid: pHis parallel / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Star / References: UniProt: Q8WX94

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HNCA
1323D HN(CA)CB
1423D CBCA(CO)NH
1523D HNCO
1623D HN(CA)CO
1723D HBHA(CO)NH
1823D C(CO)NH
1913D 1H-15N NOESY
11023D 1H-13C NOESY
11132D 1H-1H NOESY
11232D 1H-1H TOCSY
11332D 1H-1H COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-99% 15N] NLRP7 Pyd, 20 mM sodium phosphate, 50 mM sodium chloride, 0.25 mM TCEP, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-99% 13C; U-99% 15N] NLRP7 Pyd, 20 mM sodium phosphate, 50 mM sodium chloride, 0.25 mM TCEP, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM NLRP7 Pyd, 20 mM sodium phosphate, 50 mM sodium chloride, 0.25 mM TCEP, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMNLRP7 Pyd[U-99% 15N]1
20 mMsodium phosphate1
50 mMsodium chloride1
0.25 mMTCEP1
1.0 mMNLRP7 Pyd[U-99% 13C; U-99% 15N]2
20 mMsodium phosphate2
50 mMsodium chloride2
0.25 mMTCEP2
1.0 mMNLRP7 Pyd3
20 mMsodium phosphate3
50 mMsodium chloride3
0.25 mMTCEP3
Sample conditionsIonic strength: 0.05 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Avance IIBrukerAVANCE II5001
Bruker Avance IIBrukerAVANCE II8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, P. et al.structure solution
CNSBrunger, A. et al.refinement
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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