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- PDB-2l6a: Three-dimensional structure of the N-terminal effector PYRIN doma... -

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Basic information

Entry
Database: PDB / ID: 2l6a
TitleThree-dimensional structure of the N-terminal effector PYRIN domain of NLRP12
ComponentsNACHT, LRR and PYD domains-containing protein 12
KeywordsSIGNALING PROTEIN / NLRP12 / PYRIN / death domain
Function / homology
Function and homology information


regulation of interleukin-18 production / negative regulation of Toll signaling pathway / positive regulation of MHC class I biosynthetic process / regulation of cysteine-type endopeptidase activity involved in apoptotic process / dendritic cell migration / negative regulation of protein autophosphorylation / negative regulation of interleukin-1 production / negative regulation of non-canonical NF-kappaB signal transduction / regulation of canonical NF-kappaB signal transduction / negative regulation of cytokine production ...regulation of interleukin-18 production / negative regulation of Toll signaling pathway / positive regulation of MHC class I biosynthetic process / regulation of cysteine-type endopeptidase activity involved in apoptotic process / dendritic cell migration / negative regulation of protein autophosphorylation / negative regulation of interleukin-1 production / negative regulation of non-canonical NF-kappaB signal transduction / regulation of canonical NF-kappaB signal transduction / negative regulation of cytokine production / negative regulation of NF-kappaB transcription factor activity / cellular response to cytokine stimulus / cysteine-type endopeptidase activator activity involved in apoptotic process / negative regulation of interleukin-6 production / negative regulation of signal transduction / negative regulation of canonical NF-kappaB signal transduction / ERK1 and ERK2 cascade / positive regulation of interleukin-1 beta production / negative regulation of ERK1 and ERK2 cascade / negative regulation of inflammatory response / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / activation of cysteine-type endopeptidase activity involved in apoptotic process / protein-macromolecule adaptor activity / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / ATP binding / cytoplasm / cytosol
Similarity search - Function
NACHT-associated domain / Fish-specific NACHT associated domain / Fish-specific NACHT associated 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 ...NACHT-associated domain / Fish-specific NACHT associated domain / Fish-specific NACHT associated 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 / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Leucine-rich repeat profile. / Death-like domain superfamily / Leucine-rich repeat / 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 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsPinheiro, A.S. / Peti, W.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The NLRP12 pyrin domain: structure, dynamics, and functional insights.
Authors: Pinheiro, A.S. / Eibl, C. / Ekman-Vural, Z. / Schwarzenbacher, R. / Peti, W.
History
DepositionNov 17, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _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 15, 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 12


Theoretical massNumber of molelcules
Total (without water)11,7211
Polymers11,7211
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 12 / Monarch-1 / PYRIN-containing APAF1-like protein 7 / Regulated by nitric oxide


Mass: 11721.418 Da / Num. of mol.: 1 / Fragment: UNP residues 1-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLRP12, NALP12, PYPAF7, RNO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-RIL / References: UniProt: P59046

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D HNCA
1423D HN(CA)CB
1523D CBCA(CO)NH
1623D HNCO
1723D HN(CA)CO
1823D HBHA(CO)NH
1923D C(CO)NH
11023D (H)CCH-TOCSY
11113D 1H-15N NOESY
11223D 1H-13C NOESY
11332D 1H-1H NOESY
11432D 1H-1H TOCSY
11532D 1H-1H COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1600 uM [U-99% 15N] NLRP12 PYD-1, 20 mM sodium phosphate-2, 500 mM sodium chloride-3, 0.5 mM TCEP-4, 90% H2O/10% D2O90% H2O/10% D2O
2600 uM [U-99% 13C; U-99% 15N] NLRP12 PYD-5, 20 mM sodium phosphate-6, 500 mM sodium chloride-7, 0.5 mM TCEP-8, 90% H2O/10% D2O90% H2O/10% D2O
3600 uM NLRP12 PYD-9, 20 mM sodium phosphate-10, 500 mM sodium chloride-11, 0.5 mM TCEP-12, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMNLRP12 PYD-1[U-99% 15N]1
20 mMsodium phosphate-21
500 mMsodium chloride-31
0.5 mMTCEP-41
600 uMNLRP12 PYD-5[U-99% 13C; U-99% 15N]2
20 mMsodium phosphate-62
500 mMsodium chloride-72
0.5 mMTCEP-82
600 uMNLRP12 PYD-93
20 mMsodium phosphate-103
500 mMsodium chloride-113
0.5 mMTCEP-123
Sample conditionsIonic strength: 0.5 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Refinement was done in explicit solvent using CNS and the RECOORD script package.
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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