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- PDB-4n1k: Crystal structures of NLRP14 pyrin domain reveal a conformational... -

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Basic information

Entry
Database: PDB / ID: 4n1k
TitleCrystal structures of NLRP14 pyrin domain reveal a conformational switch mechanism, regulating its molecular interactions
ComponentsNACHT, LRR and PYD domains-containing protein 14
KeywordsSIGNALING PROTEIN / death domain fold / pyrin domain / NOD-like receptor / protein binding / spermatogenesis / innate immunity
Function / homology
Function and homology information


regulation of inflammatory response / spermatogenesis / cell differentiation / ATP binding / cytoplasm
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 / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / 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 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsEibl, C. / Hessenberger, M. / Wenger, J. / Brandstetter, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structures of the NLRP14 pyrin domain reveal a conformational switch mechanism regulating its molecular interactions.
Authors: Eibl, C. / Hessenberger, M. / Wenger, J. / Brandstetter, H.
History
DepositionOct 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NACHT, LRR and PYD domains-containing protein 14
B: NACHT, LRR and PYD domains-containing protein 14
C: NACHT, LRR and PYD domains-containing protein 14
D: NACHT, LRR and PYD domains-containing protein 14


Theoretical massNumber of molelcules
Total (without water)48,9964
Polymers48,9964
Non-polymers00
Water23413
1
A: NACHT, LRR and PYD domains-containing protein 14
B: NACHT, LRR and PYD domains-containing protein 14


Theoretical massNumber of molelcules
Total (without water)24,4982
Polymers24,4982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-14 kcal/mol
Surface area10750 Å2
MethodPISA
2
C: NACHT, LRR and PYD domains-containing protein 14
D: NACHT, LRR and PYD domains-containing protein 14


Theoretical massNumber of molelcules
Total (without water)24,4982
Polymers24,4982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-12 kcal/mol
Surface area10970 Å2
MethodPISA
3
A: NACHT, LRR and PYD domains-containing protein 14
B: NACHT, LRR and PYD domains-containing protein 14

C: NACHT, LRR and PYD domains-containing protein 14
D: NACHT, LRR and PYD domains-containing protein 14


Theoretical massNumber of molelcules
Total (without water)48,9964
Polymers48,9964
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_454y-1,-x+y,z-1/21
Buried area6280 Å2
ΔGint-51 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.210, 89.210, 106.571
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
NACHT, LRR and PYD domains-containing protein 14 / Nucleotide-binding oligomerization domain protein 5


Mass: 12249.041 Da / Num. of mol.: 4 / Fragment: UNP residues 1-100 / Mutation: D86V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLRP14, NALP14, NOD5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: Q86W24
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Cesium chloride and 2.2 M Ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 3, 2012 / Details: mirrors
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3→44.54 Å / Num. obs: 9722 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 %

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Processing

Software
NameVersionClassification
MAR345data collection
PHENIX(phenix.refine: 1.8.3_1479)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NLRP14 WT Ser6-Pro67

Resolution: 3→32 Å / SU ML: 0.47 / σ(F): 1.34 / Phase error: 31.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 467 4.82 %
Rwork0.2138 --
obs0.2162 9697 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3000 0 0 13 3013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023072
X-RAY DIFFRACTIONf_angle_d0.8114120
X-RAY DIFFRACTIONf_dihedral_angle_d10.9491184
X-RAY DIFFRACTIONf_chiral_restr0.027430
X-RAY DIFFRACTIONf_plane_restr0.002514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.43420.33491690.29633044X-RAY DIFFRACTION100
3.4342-4.32620.27111560.22893060X-RAY DIFFRACTION100
4.3262-44.60980.23781420.17793126X-RAY DIFFRACTION100

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