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- PDB-5irm: Crystal structure of rabbit NOD2 in an ADP-bound state (Crystal form2) -

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Basic information

Entry
Database: PDB / ID: 5irm
TitleCrystal structure of rabbit NOD2 in an ADP-bound state (Crystal form2)
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 / negative regulation of T cell mediated immunity / regulation of neutrophil chemotaxis / negative regulation of interleukin-18 production / positive regulation of dendritic cell antigen processing and presentation / host-mediated regulation of intestinal microbiota composition / intestinal stem cell homeostasis ...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 / negative regulation of T cell mediated immunity / regulation of neutrophil chemotaxis / negative regulation of interleukin-18 production / positive regulation of dendritic cell antigen processing and presentation / host-mediated regulation of intestinal microbiota composition / intestinal stem cell homeostasis / negative regulation of toll-like receptor 2 signaling pathway / regulation of appetite / toll-like receptor 2 signaling pathway / negative regulation of macrophage cytokine production / negative regulation of macrophage apoptotic process / antibacterial innate immune response / positive regulation of humoral immune response mediated by circulating immunoglobulin / maintenance of gastrointestinal epithelium / positive regulation of mitophagy / positive regulation of xenophagy / xenophagy / positive regulation of protein K63-linked ubiquitination / positive regulation of type 2 immune response / positive regulation of B cell activation / cellular response to muramyl dipeptide / CARD domain binding / peptidoglycan binding / cellular response to peptidoglycan / negative regulation of interleukin-12 production / positive regulation of cytokine production involved in inflammatory response / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of monocyte chemotactic protein-1 production / positive regulation of macrophage cytokine production / pattern recognition receptor activity / negative regulation of interleukin-2 production / temperature homeostasis / extrinsic component of plasma membrane / response to exogenous dsRNA / positive regulation of Notch signaling pathway / positive regulation of interleukin-17 production / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of interleukin-10 production / response to muramyl dipeptide / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / positive regulation of phagocytosis / phagocytic vesicle / phagocytosis / JNK cascade / negative regulation of inflammatory response to antigenic stimulus / ERK1 and ERK2 cascade / Hsp70 protein binding / detection of bacterium / positive regulation of interleukin-12 production / response to endoplasmic reticulum stress / innate immune response in mucosa / ubiquitin binding / positive regulation of interleukin-1 beta production / positive regulation of epithelial cell proliferation / positive regulation of interleukin-8 production / ADP binding / establishment of localization in cell / positive regulation of JNK cascade / Hsp90 protein binding / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / actin binding / basolateral plasma membrane / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / cytoskeleton / defense response to bacterium / protein-containing complex binding / protein kinase binding / Golgi apparatus / cell surface / 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 / Leucine rich repeat, ribonuclease inhibitor type / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Leucine Rich repeat / CARD domain ...NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / Leucine rich repeat, ribonuclease inhibitor type / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Leucine Rich repeat / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Leucine-rich repeat profile. / Death-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
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: 3.31 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,6124
Polymers183,7572
Non-polymers8542
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-8 kcal/mol
Surface area61550 Å2
Unit cell
Length a, b, c (Å)112.153, 122.870, 177.555
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 193 - 1020 / Label seq-ID: 3 - 830

Dom-IDAuth asym-IDLabel asym-ID
1AA
2CB

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Components

#1: Protein Uncharacterized protein / NOD2


Mass: 91878.695 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 194-1020
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 / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 3.4 Å3/Da / Density % sol: 63.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 5% PEG 10000, 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: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 35238 / % possible obs: 100 % / Redundancy: 6.1 % / Net I/σ(I): 8.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 3.31→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.907 / SU B: 42.734 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R Free: 0.467 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23681 1853 5 %RANDOM
Rwork0.19293 ---
obs0.19511 35238 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 78.991 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0 Å2
2--0.3 Å2-0 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 3.31→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11987 0 54 0 12041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01912269
X-RAY DIFFRACTIONr_bond_other_d0.0050.0211850
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.9716625
X-RAY DIFFRACTIONr_angle_other_deg1.184327152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.16851525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.22524.05558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.749152092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0321579
X-RAY DIFFRACTIONr_chiral_restr0.0630.21913
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213895
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022906
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_it3.9757.1216136
X-RAY DIFFRACTIONr_mcbond_other3.9737.126135
X-RAY DIFFRACTIONr_mcangle_it6.34910.6737649
X-RAY DIFFRACTIONr_mcangle_other6.34910.6747650
X-RAY DIFFRACTIONr_scbond_it4.1497.4456133
X-RAY DIFFRACTIONr_scbond_other4.1497.4456133
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.81511.0218976
X-RAY DIFFRACTIONr_long_range_B_refined11.39966.86450259
X-RAY DIFFRACTIONr_long_range_B_other11.39966.86650260
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 92350 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2C
LS refinement shellResolution: 3.31→3.395 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 139 -
Rwork0.269 2394 -
obs--92.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.17270.0807-0.12650.1471-0.03740.10770.0164-0.0351-0.0208-0.0179-0.051-0.0049-0.03840.01810.03460.0722-0.0032-0.01010.0205-0.010.075112.67771.09678.3313
20.12-0.06860.09940.22840.13330.2786-0.0590.0349-0.020.03450.0120.0796-0.03410.08490.04690.03130.00870.00580.0898-0.00440.046827.113813.595653.1877
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A193 - 1020
2X-RAY DIFFRACTION2C193 - 1020

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