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- PDB-6gwm: Solution structure of rat RIP2 caspase recruitment domain -

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Basic information

Entry
Database: PDB / ID: 6gwm
TitleSolution structure of rat RIP2 caspase recruitment domain
ComponentsReceptor-interacting serine/threonine-protein kinase 2
KeywordsSIGNALING PROTEIN / RIP2 / CARD / caspase recruitment domain / rattus norvegicus
Function / homology
Function and homology information


positive regulation of immature T cell proliferation / NOD1/2 Signaling Pathway / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Ovarian tumor domain proteases / Interleukin-1 signaling / : / p75NTR recruits signalling complexes / TAK1-dependent IKK and NF-kappa-B activation / : ...positive regulation of immature T cell proliferation / NOD1/2 Signaling Pathway / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Ovarian tumor domain proteases / Interleukin-1 signaling / : / p75NTR recruits signalling complexes / TAK1-dependent IKK and NF-kappa-B activation / : / response to interleukin-18 / positive regulation of T-helper 1 cell differentiation / toll-like receptor 2 signaling pathway / protein serine/threonine kinase activity => GO:0004674 / positive regulation of cytokine-mediated signaling pathway / positive regulation of T-helper 1 type immune response / positive regulation of xenophagy / LIM domain binding / positive regulation of alpha-beta T cell proliferation / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of stress-activated MAPK cascade / cellular response to muramyl dipeptide / CARD domain binding / caspase binding / JUN kinase kinase kinase activity / cellular response to peptidoglycan / response to interleukin-12 / activation of cysteine-type endopeptidase activity / nucleotide-binding oligomerization domain containing 2 signaling pathway / toll-like receptor 4 signaling pathway / response to exogenous dsRNA / cellular response to lipoteichoic acid / canonical NF-kappaB signal transduction / T cell proliferation / positive regulation of chemokine production / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-2 production / response to interleukin-1 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-1 beta production / positive regulation of protein ubiquitination / positive regulation of JNK cascade / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of type II interferon production / positive regulation of protein binding / positive regulation of peptidyl-serine phosphorylation / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / cellular response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / vesicle / positive regulation of ERK1 and ERK2 cascade / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / defense response to Gram-positive bacterium / positive regulation of apoptotic process / innate immune response / protein serine kinase activity / signaling receptor binding / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Receptor-interacting serine/threonine-protein kinase 2 / RIP2, CARD domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Receptor-interacting serine/threonine-protein kinase 2 / RIP2, CARD domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Receptor-interacting serine/threonine-protein kinase 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS ONFORMERS, NUMBER CALCULATED : NULL
AuthorsMineev, K.S. / Goncharuk, S.A. / Artemieva, L.E. / Arseniev, A.S.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation14-14-00573 Russian Federation
CitationJournal: PLoS ONE / Year: 2018
Title: CARD domain of rat RIP2 kinase: Refolding, solution structure, pH-dependent behavior and protein-protein interactions.
Authors: Goncharuk, S.A. / Artemieva, L.E. / Tabakmakher, V.M. / Arseniev, A.S. / Mineev, K.S.
History
DepositionJun 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor-interacting serine/threonine-protein kinase 2


Theoretical massNumber of molelcules
Total (without water)14,0751
Polymers14,0751
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8960 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Receptor-interacting serine/threonine-protein kinase 2 / Tyrosine-protein kinase RIPK2


Mass: 14075.079 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MHHHHHHGSGSGLVPRGS - polyhistidine tag with the trombine cleavage site
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ripk2, rCG_54865 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: G3V783, non-specific serine/threonine protein kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic13D HNCO
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HN(CO)CA
171isotropic13D HN(CA)CO
161isotropic13D 1H-15N NOESY
181isotropic13D 1H-13C NOESY aliphatic
191isotropic13D (H)CCH-TOCSY
1101isotropic13D (H)CCH-COSY
NMR detailsText: NULL

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-99% 13C; U-99% 15N] CARD domain of rat RIP2, 1 mM TCEP, 0.001 % sodium azide, 90% H2O/10% D2O
Label: smaple1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMCARD domain of rat RIP2[U-99% 13C; U-99% 15N]1
1 mMTCEPnatural abundance1
0.001 %sodium azidenatural abundance1
Sample conditionsIonic strength: NULL mM / Ionic strength err: 2 / Label: cond1 / pH: 4.2 / Pressure: AMBIENT Pa / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert P.structure calculation
CARA1.9.4Keller and Wuthrichchemical shift assignment
TopSpin3.2Bruker Biospinprocessing
RefinementMethod: TORSION ANGLE DYNAMICS ONFORMERS, NUMBER CALCULATED : NULL
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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