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 / 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
Deposition
Nov 9, 2017
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Header (metadata) release
Nov 14, 2018
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Map release
Nov 14, 2018
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Update
Mar 27, 2024
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Current status
Mar 27, 2024
Processing site: PDBj / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
Vitrification
Cryogen name: METHANE
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Electron microscopy
Microscope
FEI POLARA 300
Image recording
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 3 / Number real images: 3100 / Average electron dose: 8.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics
Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Model: Tecnai Polara / Image courtesy: FEI Company
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Image processing
Final reconstruction
Applied symmetry - Helical parameters - Δz: 4.936 Å Applied symmetry - Helical parameters - Δ&Phi: -101.373 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0beta) Details: Model building was based on a cropped-out density segment. Pseudo-crystallographic refinement showed that the central segment of the map is good until 3.5-3.7 A. Number images used: 142330
Segment selection
Number selected: 658160
Startup model
Type of model: OTHER Details: A tubular cylinder with 80 A width was used as the starting model.
Final angle assignment
Type: NOT APPLICABLE / Software - Name: RELION (ver. 2.0beta)
FSC plot (resolution estimation)
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Atomic model buiding 1
Refinement
Space: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 202.7 / Target criteria: Rfree value
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