9HR9 | pdb_00009hr9

SSNMR structure of amyloid fibrils formed by human RIPK1

• PDB DOI: https://doi.org/10.2210/pdb9HR9/pdb
• BMRB: 34971

• Classification: PROTEIN FIBRIL
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-12-17 Released: 2025-09-17 
• Deposition Author(s): Polonio, P., Escobedo-Gonzales, F.C., Titaux-Delgado, G.A., Mompean, M.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: SOLID-STATE NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: target function 

Literature

Resonance assignments of the human receptor interacting protein kinase 1 (RIPK1) in its fibrillar conformation.

Polonio, P., Mompean, M.

(2025) Biomol NMR Assign 19: 299-304

• PubMed: 40952585 
• DOI: https://doi.org/10.1007/s12104-025-10249-y
• Primary Citation Related Structures: 
  9HR9


• PubMed Abstract: 
  

  Receptor-interacting protein kinase 1 (RIPK1) is a key regulator of necroptotic signalling that forms functional amyloid fibrils through its RIP Homotypic Interaction Motif (RHIM). Here, we report the solid-state NMR chemical shift assignments for the rigid amyloid core of human RIPK1 fibrils, encompassing residues 529-552 within the RHIM. Assignments were obtained from uniformly ¹³ C, ¹⁵ N-labeled protein diluted with unlabeled protein and measured using cross-polarization magic angle spinning (CPMAS) experiments on a cryogenic probe. The dataset includes backbone and side-chain resonances for the ordered region and provides a basis for high-resolution structural and dynamics studies of RIPK1 and related RHIM-containing assemblies.

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Organizational Affiliation: 
• Instituto de Química Física "Blas Cabrera" - Consejo Superior de Investigaciones Científicas (IQF-CSIC), Serrano 119, Madrid, 28006, Spain. [e-mail].
Universidad Autónoma de Madrid, Escuela de Doctorado, Francisco Tomás y Valiente 2, Madrid, 28049, Spain. [e-mail].
Instituto de Química Física "Blas Cabrera" - Consejo Superior de Investigaciones Científicas (IQF-CSIC), Serrano 119, Madrid, 28006, Spain. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 2.51 kDa 
• Atom Count: 176 
• Modeled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-interacting serine/threonine-protein kinase 1	A	22	Homo sapiens	Mutation(s): 0  Gene Names: RIPK1, RIP, RIP1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13546 (Homo sapiens) Explore Q13546  Go to UniProtKB:  Q13546
PHAROS:  Q13546 GTEx:  ENSG00000137275

Experimental Data & Validation

Experimental Data

• Method: SOLID-STATE NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: target function 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): Polonio, P., Escobedo-Gonzales, F.C., Titaux-Delgado, G.A., Mompean, M.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101042403

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release
  
• Version 1.1: 2025-10-01
  Changes: Database references
• Version 1.2: 2025-10-22
  Changes: Database references