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- PDB-5irl: Crystal structure of rabbit NOD2 SER mutant in an ADP-bound state -

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Basic information

Entry
Database: PDB / ID: 5irl
TitleCrystal structure of rabbit NOD2 SER mutant in an ADP-bound state
ComponentsUncharacterized protein
KeywordsIMMUNE SYSTEM / NOD2 / innate immunity
Function / homology
Function and homology information


biosynthetic process of antibacterial peptides active against Gram-positive bacteria / detection of muramyl dipeptide / muramyl dipeptide binding / positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria / regulation of neutrophil chemotaxis / negative regulation of interleukin-18 production / negative regulation of T cell mediated immunity / host-mediated modulation of intestinal microbiota composition / positive regulation of dendritic cell antigen processing and presentation / negative regulation of toll-like receptor 2 signaling pathway ...biosynthetic process of antibacterial peptides active against Gram-positive bacteria / detection of muramyl dipeptide / muramyl dipeptide binding / positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria / regulation of neutrophil chemotaxis / negative regulation of interleukin-18 production / negative regulation of T cell mediated immunity / host-mediated modulation of intestinal microbiota composition / positive regulation of dendritic cell antigen processing and presentation / negative regulation of toll-like receptor 2 signaling pathway / regulation of appetite / toll-like receptor 2 signaling pathway / negative regulation of macrophage apoptotic process / intestinal stem cell homeostasis / positive regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of macrophage cytokine production / maintenance of gastrointestinal epithelium / positive regulation of mitophagy / antibacterial innate immune response / positive regulation of B cell activation / positive regulation of xenophagy / xenophagy / positive regulation of protein K63-linked ubiquitination / cellular response to muramyl dipeptide / positive regulation of stress-activated MAPK cascade / positive regulation of type 2 immune response / CARD domain binding / cellular response to peptidoglycan / peptidoglycan binding / negative regulation of interleukin-12 production / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of monocyte chemotactic protein-1 production / positive regulation of cytokine production involved in inflammatory response / extrinsic component of plasma membrane / positive regulation of macrophage cytokine production / negative regulation of interleukin-2 production / temperature homeostasis / positive regulation of Notch signaling pathway / pattern recognition receptor activity / positive regulation of interleukin-17 production / response to exogenous dsRNA / response to muramyl dipeptide / negative regulation of type II interferon production / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / phagocytosis / detection of bacterium / stress-activated MAPK cascade / positive regulation of phagocytosis / phagocytic vesicle / JNK cascade / positive regulation of interleukin-12 production / ERK1 and ERK2 cascade / Hsp70 protein binding / innate immune response in mucosa / response to endoplasmic reticulum stress / positive regulation of epithelial cell proliferation / ubiquitin binding / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / establishment of localization in cell / positive regulation of JNK cascade / Hsp90 protein binding / negative regulation of inflammatory response to antigenic stimulus / positive regulation of non-canonical NF-kappaB signal transduction / ADP binding / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / actin binding / cellular response to lipopolysaccharide / basolateral plasma membrane / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction / cytoskeleton / positive regulation of ERK1 and ERK2 cascade / defense response to bacterium / protein-containing complex binding / protein kinase binding / cell surface / Golgi apparatus / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / ATP binding / cytosol
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 / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat ...: / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Death-like domain superfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Nucleotide-binding oligomerization domain-containing protein 2
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.09 Å
AuthorsMaekawa, S. / Ohto, U. / Shimizu, T.
CitationJournal: Nat Commun / Year: 2016
Title: Crystal structure of NOD2 and its implications in human disease.
Authors: Maekawa, S. / Ohto, U. / Shibata, T. / Miyake, K. / Shimizu, T.
History
DepositionMar 14, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1902
Polymers91,7631
Non-polymers4271
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.900, 107.845, 185.365
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein / NOD2


Mass: 91762.617 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 194-1020 / Mutation: E943A, E944A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: NOD2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G1T469
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 4.24 Å3/Da / Density % sol: 71.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 5% PEG 20000, 5% MPD, 100 mM Hepes pH 7.8, 500 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.979 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.09→93.22 Å / Num. obs: 27203 / % possible obs: 98.8 % / Redundancy: 4.1 % / Net I/σ(I): 12.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 3.09→93.22 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.9 / SU B: 16.64 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R: 0.768 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25026 1457 5.1 %RANDOM
Rwork0.1985 ---
obs0.20113 27203 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.592 Å2
Baniso -1Baniso -2Baniso -3
1--3.71 Å20 Å2-0 Å2
2--9.45 Å20 Å2
3----5.75 Å2
Refinement stepCycle: LAST / Resolution: 3.09→93.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5792 0 27 5 5824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195927
X-RAY DIFFRACTIONr_bond_other_d0.0010.025748
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9728028
X-RAY DIFFRACTIONr_angle_other_deg0.78313156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3865736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.50423.947266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.378151015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2491539
X-RAY DIFFRACTIONr_chiral_restr0.0680.2930
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026693
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021403
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9026.7242968
X-RAY DIFFRACTIONr_mcbond_other3.9026.7232967
X-RAY DIFFRACTIONr_mcangle_it6.26710.0633696
X-RAY DIFFRACTIONr_mcangle_other6.26610.0643697
X-RAY DIFFRACTIONr_scbond_it3.8157.1282959
X-RAY DIFFRACTIONr_scbond_other3.8157.1272960
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.39610.5394333
X-RAY DIFFRACTIONr_long_range_B_refined9.252.786605
X-RAY DIFFRACTIONr_long_range_B_other9.19952.7786606
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.095→3.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 88 -
Rwork0.324 1779 -
obs--88.23 %

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