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- PDB-2b1w: Solution structure of the NOD1 Caspase Activating and Recruitment... -

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Basic information

Entry
Database: PDB / ID: 2b1w
TitleSolution structure of the NOD1 Caspase Activating and Recruitment Domain
ComponentsCaspase recruitment domain protein 4CARD domain
KeywordsAPOPTOSIS / CARD4 / six-helix bundle / Caspase recruitment domain / inflammation / NF-kB / greek key
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 / cellular response to muramyl dipeptide / CARD domain binding / peptidoglycan binding / positive regulation of macrophage cytokine production / pattern recognition receptor activity ...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 / cellular response to muramyl dipeptide / CARD domain binding / peptidoglycan binding / positive regulation of macrophage cytokine production / pattern recognition receptor activity / pattern recognition receptor signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / phagocytic vesicle / JNK cascade / ERK1 and ERK2 cascade / detection of bacterium / response to endoplasmic reticulum stress / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / ubiquitin binding / positive regulation of interleukin-1 beta production / activated TAK1 mediates p38 MAPK activation / positive regulation of interleukin-8 production / 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 interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / activation of cysteine-type endopeptidase activity involved in apoptotic process / Ovarian tumor domain proteases / positive regulation of tumor necrosis factor production / 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 / intracellular signal transduction / defense response to Gram-positive bacterium / 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 / cytosol / 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 / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Death Domain, Fas / 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 / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Death Domain, Fas / 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)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, refinement in explicit water
AuthorsManon, F. / Favier, A. / Simorre, J.P. / Cusack, S.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Solution structure of NOD1 CARD and mutational analysis of its interaction with the CARD of downstream kinase RICK.
Authors: Manon, F. / Favier, A. / Nunez, G. / Simorre, J.P. / Cusack, S.
History
DepositionSep 16, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 5, 2011Group: Database references / Other
Revision 1.4Feb 26, 2020Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.5May 1, 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

Downloads & links

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Assembly

Deposited unit
A: Caspase recruitment domain protein 4


Theoretical massNumber of molelcules
Total (without water)14,5201
Polymers14,5201
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Caspase recruitment domain protein 4 / CARD domain / Nod1 protein


Mass: 14519.569 Da / Num. of mol.: 1 / Fragment: CARD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARD4 / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: Q9Y239

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
1313D methyl selected NOESY-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.4mM NOD1 CARD 15N, 13C; 25mM phosphate buffer NA; 100mM NaCl, 5mM DTT; 95% H2O, 5% D2O95% H2O/5% D2O
21.4mM NOD1 CARD 15N; 25mM phosphate buffer NA; 100mM NaCl, 5mM DTT; 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3F.Delaglio, S.Grzesiek, G.W.Vuister, G.Zhu, J.Pfeifer, A.Baxprocessing
VNMR6.1CB.A.Johnson, R.A.Blevinscollection
CNS1.1structure solution
ARIA2M.Habeck, W.Rieping, J.P.Linge, M.Nilgesstructure solution
NMRDraw2.3F.Delaglioprocessing
ARIA2M.Habeck, W.Rieping, J.P.Linge, M.Nilgesrefinement
RefinementMethod: simulated annealing, torsion angle dynamics, refinement in explicit water
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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