|Entry||Database: EMDB / ID: 4399|
|Title||Cryo-EM structure of the RIP2 CARD filament|
|Sample||Helical assemble of the CARD domain of RIP2|
|Function / homology||Serine/Threonine protein kinases active-site signature. / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / Protein tyrosine kinase / Caspase recruitment domain / Receptor-interacting serine/threonine-protein kinase 2 / Death-like domain superfamily / Protein kinase-like domain superfamily / Serine/threonine-protein kinase, active site / CARD domain / Serine-threonine/tyrosine-protein kinase, catalytic domain ...Serine/Threonine protein kinases active-site signature. / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / Protein tyrosine kinase / Caspase recruitment domain / Receptor-interacting serine/threonine-protein kinase 2 / Death-like domain superfamily / Protein kinase-like domain superfamily / Serine/threonine-protein kinase, active site / CARD domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase domain / CARD caspase recruitment domain profile. / NOD1/2 Signaling Pathway / Downstream TCR signaling / Protein kinase domain profile. / p75NTR recruits signalling complexes / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Interleukin-1 signaling / Ovarian tumor domain proteases / activated TAK1 mediates p38 MAPK activation / positive regulation of immature T cell proliferation / nucleotide-binding oligomerization domain containing 1 signaling pathway / response to interleukin-18 / positive regulation of T-helper 1 cell differentiation / toll-like receptor 2 signaling pathway / positive regulation of cytokine-mediated signaling pathway / caspase binding / nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to peptidoglycan / positive regulation of xenophagy / cellular response to muramyl dipeptide / LIM domain binding / CARD domain binding / response to interleukin-12 / activation of cysteine-type endopeptidase activity / positive regulation of alpha-beta T cell proliferation / toll-like receptor 4 signaling pathway / positive regulation of interferon-alpha production / positive regulation of chemokine production / positive regulation of interleukin-1 beta secretion / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / response to exogenous dsRNA / positive regulation of interleukin-2 production / positive regulation of interleukin-6 production / T cell proliferation / cellular response to lipoteichoic acid / positive regulation of tumor necrosis factor production / nucleotide-binding oligomerization domain containing signaling pathway / positive regulation of protein ubiquitination / positive regulation of cell death / positive regulation of peptidyl-threonine phosphorylation / positive regulation of JNK cascade / lipopolysaccharide-mediated signaling pathway / interleukin-1-mediated signaling pathway / JNK cascade / positive regulation of interferon-gamma production / I-kappaB kinase/NF-kappaB signaling / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / positive regulation of peptidyl-tyrosine phosphorylation / T cell receptor signaling pathway / adaptive immune response / positive regulation of peptidyl-serine phosphorylation / positive regulation of I-kappaB kinase/NF-kappaB signaling / vesicle / positive regulation of protein binding / activation of MAPK activity / cytoskeleton / positive regulation of ERK1 and ERK2 cascade / MAPK cascade / positive regulation of NF-kappaB transcription factor activity / non-specific serine/threonine protein kinase / defense response to Gram-positive bacterium / inflammatory response / positive regulation of apoptotic process / apoptotic process / signaling receptor binding / protein serine/threonine kinase activity / innate immune response / negative regulation of apoptotic process / signal transduction / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / cytosol / cytoplasm / Receptor-interacting serine/threonine-protein kinase 2|
Function and homology information
|Source||Homo sapiens (human)|
|Method||helical reconstruction / cryo EM / 3.94 Å resolution|
|Authors||Pellegrini E / Cusack S / Desfosses A / Schoehn G / Malet H / Gutsche I / Sachse C / Hons M|
|Citation||Journal: 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 / Helene Malet / Irina Gutsche / Carsten Sachse / Guy Schoehn / Hartmut Oschkinat / Stephen Cusack
|Validation Report||PDB-ID: 6ggs|
SummaryFull reportAbout validation report
|Date||Deposition: May 3, 2018 / Header (metadata) release: Sep 19, 2018 / Map release: Oct 17, 2018 / Last update: Oct 17, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_4399.map.gz (map file in CCP4 format, 4001 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.21 Å|
CCP4 map header:
-Entire Helical assemble of the CARD domain of RIP2
|Entire||Name: Helical assemble of the CARD domain of RIP2 / Number of components: 2|
-Component #1: protein, Helical assemble of the CARD domain of RIP2
|Protein||Name: Helical assemble of the CARD domain of RIP2 / Recombinant expression: No|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: escherichia coli (E. coli)|
-Component #2: protein, Receptor-interacting serine/threonine-protein kinase 2
|Protein||Name: Receptor-interacting serine/threonine-protein kinase 2|
Number of Copies: 10 / Recombinant expression: No
|Mass||Theoretical: 12.572368 kDa|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
|Specimen||Specimen state: helical array / Method: cryo EM|
|Helical parameters||Axial symmetry: C1 (asymmetric) / Delta z: 4.848 Å / Delta phi: -101.12 deg.|
|Sample solution||pH: 7.5|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Imaging||Microscope: FEI POLARA 300|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.25 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 QUANTUM (4k x 4k)|
|Processing||Method: helical reconstruction|
|3D reconstruction||Software: SPRING / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF|
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