|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/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 / positive regulation of alpha-beta T cell proliferation / activation of cysteine-type endopeptidase activity / 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 cell death / positive regulation of peptidyl-threonine phosphorylation / 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 / 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|
-Atomic model buiding
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
-Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi