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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6663 | |||||||||
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Title | Structure of RIP2 CARD domain | |||||||||
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Biological species | ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.85 Å | |||||||||
![]() | Wu B / Gong Q | |||||||||
![]() | ![]() 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 / ![]() ![]() ![]() ![]() ![]() Abstract: Signals arising from bacterial infections are detected by pathogen recognition receptors (PRRs) and are transduced by specialized adapter proteins in mammalian cells. The Receptor-interacting- ...Signals arising from bacterial infections are detected by pathogen recognition receptors (PRRs) and are transduced by specialized adapter proteins in mammalian cells. The Receptor-interacting-serine/threonine-protein kinase 2 (RIPK2 or RIP2) is such an adapter protein that is critical for signal propagation of the Nucleotide-binding-oligomerization-domain-containing proteins 1/2 (NOD1 and NOD2). Dysregulation of this signaling pathway leads to defects in bacterial detection and in some cases autoimmune diseases. Here, we show that the Caspase-activation-and-recruitment-domain (CARD) of RIP2 (RIP2-CARD) forms oligomeric structures upon stimulation by either NOD1-CARD or NOD2-2CARD. We reconstitute this complex, termed the RIPosome in vitro and solve the cryo-EM filament structure of the active RIP2-CARD complex at 4.1 Å resolution. The structure suggests potential mechanisms by which CARD domains from NOD1 and NOD2 initiate the oligomerization process of RIP2-CARD. Together with structure guided mutagenesis experiments at the CARD-CARD interfaces, we demonstrate molecular mechanisms how RIP2 is activated and self-propagating such signal. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 28 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.8 KB 13.8 KB | Display Display | ![]() |
Images | ![]() | 98 KB | ||
Others | ![]() ![]() | 23.3 MB 23.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 638.3 KB | Display | ![]() |
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Full document | ![]() | 637.9 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 12.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5h4a ![]() 6842C ![]() 5yrnC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_6663_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_6663_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Active RIP2 signaling complex
Entire | Name: Active RIP2 signaling complex |
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Components |
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-Supramolecule #1: Active RIP2 signaling complex
Supramolecule | Name: Active RIP2 signaling complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Receptor-interacting serine/threonine-protein kinase 2
Macromolecule | Name: Receptor-interacting serine/threonine-protein kinase 2 type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 10.751217 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: TNSAGIAQQW IQSKREDIVN QMTEACLNQS LDALLSRDLI MKEDYELVST KPTRTSKVRQ LLDTTDIQGE EFAKVIVQKL KDNKQMGLQ PYPEI |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.4 |
Grid | Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: METHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 12.6 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 4.9448 Å Applied symmetry - Helical parameters - Δ&Phi: -101.188 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 4.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0beta) Details: The model is only a partial model. Indefinite filament model could be produced by a helical rotation. Number images used: 118954 |
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CTF correction | Software - Name: RELION (ver. 2.0beta) |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: RELION (ver. 2.0beta) |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | ![]()
PDB-5h4a: |