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- PDB-2nsn: Crystal structure of Caspace Activation and Recruitment Domain (C... -

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Basic information

Entry
Database: PDB / ID: 2nsn
TitleCrystal structure of Caspace Activation and Recruitment Domain (CARD) of NOD1
ComponentsCaspase recruitment domain-containing protein 4
KeywordsAPOPTOSIS / Six helix greek key motif
Function / homology
Function and homology information


positive regulation of dendritic cell antigen processing and presentation / detection of biotic stimulus / positive regulation of xenophagy / xenophagy / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of stress-activated MAPK cascade / cellular response to muramyl dipeptide / CARD domain binding / peptidoglycan binding / positive regulation of macrophage cytokine production ...positive regulation of dendritic cell antigen processing and presentation / detection of biotic stimulus / positive regulation of xenophagy / xenophagy / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of stress-activated MAPK cascade / cellular response to muramyl dipeptide / CARD domain binding / peptidoglycan binding / positive regulation of macrophage cytokine production / pattern recognition receptor signaling pathway / pattern recognition receptor activity / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / detection of bacterium / stress-activated MAPK cascade / JNK cascade / ERK1 and ERK2 cascade / phagocytic vesicle / response to endoplasmic reticulum stress / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of interleukin-1 beta production / ubiquitin binding / positive regulation of interleukin-8 production / activated TAK1 mediates p38 MAPK activation / positive regulation of JNK cascade / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / defense response / Interleukin-1 signaling / positive regulation of non-canonical NF-kappaB signal transduction / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / Ovarian tumor domain proteases / positive regulation of NF-kappaB transcription factor activity / basolateral plasma membrane / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / intracellular signal transduction / defense response to bacterium / inflammatory response / positive regulation of apoptotic process / apical plasma membrane / innate immune response / apoptotic process / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / protein homodimerization activity / ATP binding / identical protein binding / plasma membrane / cytoplasm / 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 / Death Domain, Fas / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Death Domain, Fas / Leucine rich repeat, ribonuclease inhibitor type ...NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / Death Domain, Fas / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Death Domain, Fas / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / 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
Nucleotide-binding oligomerization domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRamaswamy, S. / Coussens, N.P.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: Crystal structure of the Nod1 caspase activation and recruitment domain.
Authors: Coussens, N.P. / Mowers, J.C. / McDonald, C. / Nunez, G. / Ramaswamy, S.
History
DepositionNov 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Caspase recruitment domain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)10,9781
Polymers10,9781
Non-polymers00
Water64936
1
A: Caspase recruitment domain-containing protein 4

A: Caspase recruitment domain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)21,9552
Polymers21,9552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3510 Å2
ΔGint-23 kcal/mol
Surface area9770 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)40.141, 40.141, 150.748
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsThe second part of the biolgical assembly is generated by the two fold axis -y,-x,-z+1/2

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Components

#1: Protein Caspase recruitment domain-containing protein 4 / Protein Nod1


Mass: 10977.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARD4, NOD1 / Plasmid: PET 21A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL 21 DE3 / References: UniProt: Q9Y239
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.7
Details: 15% PEG 3000, 100mM acetate, 20mgs/ml protein, pH 4.7, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→28.38 Å / Num. all: 9009 / Num. obs: 8946 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.26 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.059 / Χ2: 1 / Net I/σ(I): 21.3 / Scaling rejects: 897
Reflection shellResolution: 2→2.07 Å / Redundancy: 13.13 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 4.8 / Num. measured all: 11350 / Num. unique all: 862 / Χ2: 0.77 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
d*TREK9.6Ldata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
StructureStudiodata collection
d*TREKdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DGN

1dgn


Resolution: 2→10.78 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.947 / SU B: 9.242 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 418 4.7 %RANDOM
Rwork0.221 ---
obs0.222 8874 99.38 %-
all-9009 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 63.506 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å20 Å2
2--1.75 Å20 Å2
3----3.5 Å2
Refinement stepCycle: LAST / Resolution: 2→10.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms771 0 0 36 807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022785
X-RAY DIFFRACTIONr_bond_other_d0.0070.02524
X-RAY DIFFRACTIONr_angle_refined_deg1.341.9831066
X-RAY DIFFRACTIONr_angle_other_deg0.99731290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.055594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.68825.38539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65215143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.518154
X-RAY DIFFRACTIONr_chiral_restr0.090.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02855
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02144
X-RAY DIFFRACTIONr_nbd_refined0.2150.2159
X-RAY DIFFRACTIONr_nbd_other0.1630.2511
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2381
X-RAY DIFFRACTIONr_nbtor_other0.0930.2393
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.223
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0810.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.25
X-RAY DIFFRACTIONr_mcbond_it0.8721.5626
X-RAY DIFFRACTIONr_mcbond_other0.151.5187
X-RAY DIFFRACTIONr_mcangle_it0.9912773
X-RAY DIFFRACTIONr_scbond_it1.683379
X-RAY DIFFRACTIONr_scangle_it2.3434.5293
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 30 -
Rwork0.273 588 -
obs-618 99.52 %
Refinement TLS params.Method: refined / Origin x: 1.5608 Å / Origin y: 9.3318 Å / Origin z: 48.3989 Å
111213212223313233
T-0.3718 Å2-0.0839 Å2-0.0009 Å2--0.1317 Å2-0.0154 Å2---0.2476 Å2
L9.3507 °2-0.933 °22.5827 °2-3.4764 °21.0749 °2--10.1316 °2
S0.0004 Å °0.5582 Å °0.3528 Å °-0.188 Å °0.0869 Å °-0.0793 Å °-0.2666 Å °0.6141 Å °-0.0873 Å °
Refinement TLS groupSelection: ALL

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