8IB0 | pdb_00008ib0

The amyloid structure of mouse RIPK1 RHIM-containing domain by solid-state NMR


Experimental Data Snapshot

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 196 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

The structure of mouse RIPK1 RHIM-containing domain as a homo-amyloid and in RIPK1/RIPK3 complex.

Liu, J.Wu, X.L.Zhang, J.Li, B.Wang, H.Y.Wang, J.Lu, J.X.

(2024) Nat Commun 15: 6975-6975

  • DOI: https://doi.org/10.1038/s41467-024-51303-y
  • Primary Citation Related Structures: 
    8IB0

  • PubMed Abstract: 

    Receptor-interacting protein kinase 1 (RIPK1) is a therapeutic target in treating neurodegenerative diseases and cancers. RIPK1 has three distinct functional domains, with the center domain containing a receptor-interacting protein homotypic interaction motif (RHIM), which mediates amyloid formation. The functional amyloid formed by RIPK1 and/or RIPK3 is a crucial intermediate in regulating cell necroptosis. In this study, the amyloid structure of mouse RIPK1, formed by an 82-residue sequence centered at RHIM, is presented. It reveals the "N"-shaped folding of the protein subunit in the fibril with four β-strands. The folding pattern is shared by several amyloid structures formed by proteins with RHIM, with the central β-strand formed by the most conserved tetrad sequence I/VQI/VG. However, the solid-state NMR results indicate a structural difference between mouse RIPK1 and mouse RIPK3. A change in the structural rigidity is also suggested by the observation of weakened signals for mouse RIPK3 upon mixing with RIPK1 to form the RIPK1/RIPK3 complex fibrils. Our results provide vital information to understand the interactions between different proteins with RHIM, which will help us further comprehend the regulation mechanism in cell necroptosis.


  • Organizational Affiliation
    • School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.

Macromolecule Content 

  • Total Structure Weight: 13.51 kDa 
  • Atom Count: 950 
  • Modeled Residue Count: 120 
  • Deposited Residue Count: 120 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Receptor-interacting serine/threonine-protein kinase 1
A, B, C, D, E
24Mus musculusMutation(s): 0 
Gene Names: Ripk1RinpRip
EC: 2.7.11.1
UniProt
Find proteins for Q60855 (Mus musculus)
Explore Q60855 
Go to UniProtKB:  Q60855
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60855
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 196 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171185

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Data collection, Database references
  • Version 1.2: 2024-08-21
    Changes: Database references
  • Version 1.3: 2024-08-28
    Changes: Database references