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- PDB-6ggs: Structure of RIP2 CARD filament -

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Basic information

Entry
Database: PDB / ID: 6ggs
TitleStructure of RIP2 CARD filament
ComponentsReceptor-interacting serine/threonine-protein kinase 2
KeywordsTRANSFERASE / CARD / RIP2 / filament / helical
Function / homology
Function and homology information


response to interleukin-18 / toll-like receptor 2 signaling pathway / positive regulation of T-helper 1 cell differentiation / positive regulation of cytokine-mediated signaling pathway / positive regulation of T-helper 1 type immune response / positive regulation of xenophagy / immature T cell proliferation in thymus / caspase binding / xenophagy / LIM domain binding ...response to interleukin-18 / toll-like receptor 2 signaling pathway / positive regulation of T-helper 1 cell differentiation / positive regulation of cytokine-mediated signaling pathway / positive regulation of T-helper 1 type immune response / positive regulation of xenophagy / immature T cell proliferation in thymus / caspase binding / xenophagy / LIM domain binding / positive regulation of protein K63-linked ubiquitination / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of stress-activated MAPK cascade / cellular response to muramyl dipeptide / CARD domain binding / positive regulation of immature T cell proliferation in thymus / CD4-positive, alpha-beta T cell proliferation / JUN kinase kinase kinase activity / cellular response to peptidoglycan / response to interleukin-12 / positive regulation of CD4-positive, alpha-beta T cell proliferation / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of macrophage cytokine production / positive regulation of peptidyl-tyrosine phosphorylation / toll-like receptor 4 signaling pathway / response to exogenous dsRNA / cellular response to lipoteichoic acid / positive regulation of interferon-alpha production / canonical NF-kappaB signal transduction / stress-activated MAPK cascade / positive regulation of chemokine production / JNK cascade / ERK1 and ERK2 cascade / signaling adaptor activity / positive regulation of interleukin-12 production / positive regulation of interleukin-2 production / p75NTR recruits signalling complexes / positive regulation of interferon-beta production / response to interleukin-1 / lipopolysaccharide-mediated signaling pathway / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of interleukin-1 beta production / positive regulation of protein ubiquitination / activated TAK1 mediates p38 MAPK activation / non-membrane spanning protein tyrosine kinase activity / positive regulation of JNK cascade / non-specific protein-tyrosine kinase / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / protein homooligomerization / positive regulation of interleukin-6 production / positive regulation of type II interferon production / Interleukin-1 signaling / cytokine-mediated signaling pathway / positive regulation of tumor necrosis factor production / Ovarian tumor domain proteases / Downstream TCR signaling / T cell receptor signaling pathway / vesicle / adaptive immune response / cytoskeleton / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / defense response to Gram-positive bacterium / defense response to bacterium / positive regulation of apoptotic process / inflammatory response / signaling receptor binding / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP binding / identical protein binding / plasma membrane / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site ...Receptor-interacting serine/threonine-protein kinase 2 / RIP2, CARD domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / : / Death-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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 speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsPellegrini, E. / Cusack, S. / Desfosses, A. / Schoehn, G. / Malet, H. / Gutsche, I. / Sachse, C. / Hons, M.
Funding support France, 1items
OrganizationGrant numberCountry
FRM-ARF20160936266 France
CitationJournal: Nat Commun / Year: 2018
Title: RIP2 filament formation is required for NOD2 dependent NF-κB signalling.
Authors: Erika Pellegrini / Ambroise Desfosses / Arndt Wallmann / Wiebke Manuela Schulze / Kristina Rehbein / Philippe Mas / Luca Signor / Stephanie Gaudon / Grasilda Zenkeviciute / Michael Hons / ...Authors: Erika Pellegrini / Ambroise Desfosses / Arndt Wallmann / Wiebke Manuela Schulze / Kristina Rehbein / Philippe Mas / Luca Signor / Stephanie Gaudon / Grasilda Zenkeviciute / Michael Hons / Helene Malet / Irina Gutsche / Carsten Sachse / Guy Schoehn / Hartmut Oschkinat / Stephen Cusack /
Abstract: Activation of the innate immune pattern recognition receptor NOD2 by the bacterial muramyl-dipeptide peptidoglycan fragment triggers recruitment of the downstream adaptor kinase RIP2, eventually ...Activation of the innate immune pattern recognition receptor NOD2 by the bacterial muramyl-dipeptide peptidoglycan fragment triggers recruitment of the downstream adaptor kinase RIP2, eventually leading to NF-κB activation and proinflammatory cytokine production. Here we show that full-length RIP2 can form long filaments mediated by its caspase recruitment domain (CARD), in common with other innate immune adaptor proteins. We further show that the NOD2 tandem CARDs bind to one end of the RIP2 CARD filament, suggesting a mechanism for polar filament nucleation by activated NOD2. We combine X-ray crystallography, solid-state NMR and high-resolution cryo-electron microscopy to determine the atomic structure of the helical RIP2 CARD filament, which reveals the intermolecular interactions that stabilize the assembly. Using structure-guided mutagenesis, we demonstrate the importance of RIP2 polymerization for the activation of NF-κB signalling by NOD2. Our results could be of use to develop new pharmacological strategies to treat inflammatory diseases characterised by aberrant NOD2 signalling.
History
DepositionMay 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Assembly

Deposited unit
F: Receptor-interacting serine/threonine-protein kinase 2
A: Receptor-interacting serine/threonine-protein kinase 2
B: Receptor-interacting serine/threonine-protein kinase 2
C: Receptor-interacting serine/threonine-protein kinase 2
D: Receptor-interacting serine/threonine-protein kinase 2
E: Receptor-interacting serine/threonine-protein kinase 2
G: Receptor-interacting serine/threonine-protein kinase 2
H: Receptor-interacting serine/threonine-protein kinase 2
I: Receptor-interacting serine/threonine-protein kinase 2
J: Receptor-interacting serine/threonine-protein kinase 2


Theoretical massNumber of molelcules
Total (without water)125,86510
Polymers125,86510
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area14430 Å2
ΔGint-35 kcal/mol
Surface area37210 Å2
MethodPISA

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Components

#1: Protein
Receptor-interacting serine/threonine-protein kinase 2 / CARD-containing interleukin-1 beta-converting enzyme-associated kinase / CARD-containing IL-1 beta ...CARD-containing interleukin-1 beta-converting enzyme-associated kinase / CARD-containing IL-1 beta ICE-kinase / RIP-like-interacting CLARP kinase / Receptor-interacting protein 2 / RIP-2 / Tyrosine-protein kinase RIPK2


Mass: 12586.478 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RIPK2, CARDIAK, RICK, RIP2, UNQ277/PRO314/PRO34092 / Production host: Escherichia coli (E. coli)
References: UniProt: O43353, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Helical assemble of the CARD domain of RIP2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.25 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM softwareName: SPRING / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -101.12 ° / Axial rise/subunit: 4.848 Å / Axial symmetry: C1
3D reconstructionResolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9661 / Symmetry type: HELICAL

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