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- PDB-2m5v: Three-dimensional structure of human NLRP10/PYNOD pyrin domain -

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Basic information

Entry
Database: PDB / ID: 2m5v
TitleThree-dimensional structure of human NLRP10/PYNOD pyrin domain
ComponentsNACHT, LRR and PYD domains-containing protein 10
KeywordsIMMUNE SYSTEM / NLRP10 / PYNOD / pyrin domain
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 / extrinsic component of plasma membrane / defense response to fungus / positive regulation of interleukin-8 production / positive regulation of inflammatory response / positive regulation of interleukin-6 production / defense response to Gram-negative bacterium ...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 / extrinsic component of plasma membrane / defense response to fungus / positive regulation of interleukin-8 production / positive regulation of inflammatory response / positive regulation of interleukin-6 production / defense response to Gram-negative bacterium / adaptive immune response / inflammatory response / innate immune response / GTPase activity / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
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 ...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 / 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 speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsSu, M.Y. / Chang, C.F. / Chang, C.I.
Citation
Journal: Plos One / Year: 2013
Title: Three-Dimensional Structure of Human NLRP10/PYNOD Pyrin Domain Reveals a Homotypic Interaction Site Distinct from Its Mouse Homologue.
Authors: Su, M.Y. / Kuo, C.I. / Chang, C.F. / Chang, C.I.
#1: Journal: Biomol.Nmr Assign. / Year: 2012
Title: (1)H, (13)C and (15)N resonance assignments of the pyrin domain from human PYNOD.
Authors: Su, M.Y. / Chang, C.I. / Chang, C.F.
History
DepositionMar 11, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Jul 31, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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 10


Theoretical massNumber of molelcules
Total (without water)11,5831
Polymers11,5831
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 10 / Nucleotide-binding oligomerization domain protein 8


Mass: 11582.622 Da / Num. of mol.: 1 / Fragment: UNP residues 1-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLRP10, NALP10, NOD8, PYNOD / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q86W26

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HNCA
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D H(CCO)NH
11113D 1H-15N TOCSY
11213D HBHA(CO)NH
11313D HN(CO)CA

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Sample preparation

DetailsContents: 0.2 mM [U-13C; U-15N] PYNOD PYD, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.2 mM / Component: PYNOD PYD-1 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 140 / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR softwareName: CYANA / Classification: refinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 969 / NOE intraresidue total count: 525 / NOE medium range total count: 179 / NOE sequential total count: 265
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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