|Entry||Database: EMDB / ID: 6842|
|Title||Structure of RIP2 CARD domain|
|Map data||200 A long segment of RIP-CARD filament|
|Sample||Active RIP2 signaling complex|
|Function / homology||Serine-threonine/tyrosine-protein kinase, catalytic domain / NOD1/2 Signaling Pathway / Protein kinase domain / Receptor-interacting serine/threonine-protein kinase 2 / Serine/threonine-protein kinase, active site / Caspase recruitment domain / Protein tyrosine kinase / CARD domain / Death-like domain superfamily / Serine/Threonine protein kinases active-site signature. ...Serine-threonine/tyrosine-protein kinase, catalytic domain / NOD1/2 Signaling Pathway / Protein kinase domain / Receptor-interacting serine/threonine-protein kinase 2 / Serine/threonine-protein kinase, active site / Caspase recruitment domain / Protein tyrosine kinase / CARD domain / Death-like domain superfamily / Serine/Threonine protein kinases active-site signature. / Protein kinase domain profile. / CARD caspase recruitment domain profile. / Protein kinase-like domain superfamily / Downstream TCR signaling / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / activated TAK1 mediates p38 MAPK activation / Interleukin-1 signaling / Ovarian tumor domain proteases / p75NTR recruits signalling complexes / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / 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 / JUN kinase kinase kinase activity / cellular response to peptidoglycan / nucleotide-binding oligomerization domain containing 2 signaling pathway / 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 chemokine production / positive regulation of interferon-alpha production / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta secretion / response to exogenous dsRNA / T cell proliferation / positive regulation of interferon-beta production / positive regulation of interleukin-2 production / cellular response to lipoteichoic acid / positive regulation of interleukin-6 production / activation of JUN kinase activity / nucleotide-binding oligomerization domain containing signaling pathway / positive regulation of tumor necrosis factor production / positive regulation of protein ubiquitination / positive regulation of peptidyl-threonine phosphorylation / positive regulation of cell death / 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 / adaptive immune response / T cell receptor signaling pathway / 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 / MAPK cascade / positive regulation of NF-kappaB transcription factor activity / non-specific serine/threonine protein kinase / defense response to Gram-positive bacterium / positive regulation of ERK1 and ERK2 cascade / inflammatory response / positive regulation of apoptotic process / apoptotic process / innate immune response / signaling receptor binding / protein serine/threonine kinase activity / signal transduction / negative regulation of apoptotic process / 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 / 4.1 Å resolution|
|Authors||Wu B / Gong Q|
|Citation||Journal: Nat Commun / Year: 2018|
Title: Structural basis of RIP2 activation and signaling.
Authors: Qin Gong / Ziqi Long / Franklin L Zhong / Daniel Eng Thiam Teo / Yibo Jin / Zhan Yin / Zhao Zhi Boo / Yaming Zhang / Jiawen Zhang / Renliang Yang / Shashi Bhushan / Bruno Reversade / Zongli Li / Bin Wu
|Validation Report||PDB-ID: 5yrn|
SummaryFull reportAbout validation report
|Date||Deposition: Nov 9, 2017 / Header (metadata) release: Nov 14, 2018 / Map release: Nov 14, 2018 / Last update: Nov 14, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_6842.map.gz (map file in CCP4 format, 32001 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.23 Å|
CCP4 map header:
-Entire Active RIP2 signaling complex
|Entire||Name: Active RIP2 signaling complex / Number of components: 2|
-Component #1: cellular-component, Active RIP2 signaling complex
|Cellular-component||Name: Active RIP2 signaling complex / Recombinant expression: No|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Escherichia coli (E. coli) / Vector: pSNAP|
-Component #2: protein, Receptor-interacting serine/threonine-protein kinase 2
|Protein||Name: Receptor-interacting serine/threonine-protein kinase 2|
Number of Copies: 12 / Recombinant expression: No
|Mass||Theoretical: 12.621438 kDa|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
|Specimen||Specimen state: filament / Method: cryo EM|
|Helical parameters||Axial symmetry: C1 (asymmetric) / Delta z: 4.936 Å / Delta phi: -101.373 deg.|
|Sample solution||Specimen conc.: 0.2 mg/ml / pH: 7.4|
|Vitrification||Cryogen name: METHANE|
-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: 8 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 3100|
-Atomic model buiding
|Modeling #1||Refinement protocol: rigid body / Target criteria: Rfree value / Refinement space: RECIPROCAL / Overall bvalue: 202.699999999999989|
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