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- PDB-9hr6: cryoEM structure of amyloid fibrils formed by human RIPK1 -

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Basic information

Entry
Database: PDB / ID: 9hr6
TitlecryoEM structure of amyloid fibrils formed by human RIPK1
ComponentsReceptor-interacting serine/threonine-protein kinase 1
KeywordsPROTEIN FIBRIL / Amyloid / kinase
Function / homology
Function and homology information


ripoptosome assembly / positive regulation of miRNA processing / positive regulation of interleukin-6-mediated signaling pathway / death domain binding / ripoptosome assembly involved in necroptotic process / programmed necrotic cell death / Defective RIPK1-mediated regulated necrosis / Microbial modulation of RIPK1-mediated regulated necrosis / ripoptosome / TRIF-mediated programmed cell death ...ripoptosome assembly / positive regulation of miRNA processing / positive regulation of interleukin-6-mediated signaling pathway / death domain binding / ripoptosome assembly involved in necroptotic process / programmed necrotic cell death / Defective RIPK1-mediated regulated necrosis / Microbial modulation of RIPK1-mediated regulated necrosis / ripoptosome / TRIF-mediated programmed cell death / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TLR3-mediated TICAM1-dependent programmed cell death / Dengue virus modulates apoptosis / activation of protein kinase activity / positive regulation of macrophage differentiation / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / T cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / JUN kinase kinase kinase activity / necroptotic signaling pathway / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / negative regulation of necroptotic process / RIP-mediated NFkB activation via ZBP1 / death-inducing signaling complex / positive regulation of necroptotic process / positive regulation of tumor necrosis factor-mediated signaling pathway / death receptor binding / positive regulation of programmed cell death / positive regulation of programmed necrotic cell death / TNFR1-induced proapoptotic signaling / positive regulation of extrinsic apoptotic signaling pathway / RIPK1-mediated regulated necrosis / necroptotic process / TRP channels / extrinsic apoptotic signaling pathway via death domain receptors / protein serine/threonine phosphatase activity / response to tumor necrosis factor / positive regulation of execution phase of apoptosis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway / canonical NF-kappaB signal transduction / signaling adaptor activity / negative regulation of extrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-8 production / negative regulation of canonical NF-kappaB signal transduction / TICAM1, RIP1-mediated IKK complex recruitment / protein serine/threonine kinase binding / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to growth factor stimulus / positive regulation of JNK cascade / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to tumor necrosis factor / Regulation of necroptotic cell death / positive regulation of reactive oxygen species metabolic process / cellular response to hydrogen peroxide / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / Ovarian tumor domain proteases / positive regulation of neuron apoptotic process / response to oxidative stress / amyloid fibril formation / Potential therapeutics for SARS / positive regulation of canonical NF-kappaB signal transduction / protein kinase activity / non-specific serine/threonine protein kinase / signaling receptor complex / endosome membrane / intracellular signal transduction / Ub-specific processing proteases / positive regulation of apoptotic process / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / positive regulation of gene expression / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein-containing complex binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
RIP1, Death domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / : / Death-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site ...RIP1, Death domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / : / Death-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Receptor-interacting serine/threonine-protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsLopez-Alonso, J.P. / Ubarretxena-Belandia, I. / Jiang, H.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for amyloid fibril assembly by the master cell-signaling regulator receptor-interacting protein kinase 1.
Authors: Paula Polonio / Jorge Pedro López-Alonso / Hanxing Jiang / Sara Andrés-Campos / Fátima C Escobedo-González / Gustavo A Titaux-Delgado / Iban Ubarretxena-Belandia / Miguel Mompeán /
Abstract: Amyloid fibrils can form biologically relevant functional assemblies. The RIP homotypic interaction motifs (RHIMs) in receptor-interacting protein kinases 1 and 3 (RIPK1 and RIPK3) orchestrate the ...Amyloid fibrils can form biologically relevant functional assemblies. The RIP homotypic interaction motifs (RHIMs) in receptor-interacting protein kinases 1 and 3 (RIPK1 and RIPK3) orchestrate the formation of amyloid-like fibrils essential for propagating cell death signals. While the structures of human RIPK3 (hRIPK3) homomeric fibrils and RIPK1-RIPK3 heteromeric fibrils have been elucidated, the atomic structure of human RIPK1 (hRIPK1) homomeric fibrils has remained elusive. We present a high-resolution structure of hRIPK1 RHIM-mediated amyloid fibrils, determined using an integrative approach combining cryoprobe-detected solid-state nuclear magnetic resonance spectroscopy and cryo-electron microscopy. The fibrils adopt an N-shaped fold consisting of three β-sheets stabilized by hydrophobic interactions and hydrogen bonding. A key hydrogen bond between N545 and G542 closes the β2-β3 loop, resulting in denser side-chain packing compared to hRIPK3 homomeric fibrils. These findings provide structural insights into how hRIPK1 homomeric fibrils nucleate hRIPK3 recruitment and fibrillization during necroptosis, offering broader perspectives on the molecular principles governing RHIM-mediated amyloid assembly and functional amyloids.
History
DepositionDec 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor-interacting serine/threonine-protein kinase 1
B: Receptor-interacting serine/threonine-protein kinase 1
C: Receptor-interacting serine/threonine-protein kinase 1
D: Receptor-interacting serine/threonine-protein kinase 1
E: Receptor-interacting serine/threonine-protein kinase 1


Theoretical massNumber of molelcules
Total (without water)48,2835
Polymers48,2835
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Receptor-interacting serine/threonine-protein kinase 1 / Cell death protein RIP / Receptor-interacting protein 1 / RIP-1


Mass: 9656.604 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RIPK1, RIP, RIP1 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q13546, non-specific serine/threonine protein kinase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: hRIPK1 RHIM-mediated amyloid fibril / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3) / Plasmid: pET11A
Buffer solutionpH: 7.5
Buffer componentConc.: 50 mM / Name: TrisHCl
SpecimenConc.: 0.765 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 9 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: time 5.5s, blotting force 2

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: LAB6 / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.88 sec. / Electron dose: 49.3 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 1
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
2EPU3.8.0.7600image acquisition
4cryoSPARC4.6.0CTF correction
9cryoSPARC4.6.0initial Euler assignment
10cryoSPARC4.6.0final Euler assignment
12cryoSPARC4.6.23D reconstruction
13Coot0.9.2model refinement
14PHENIX1.21model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -7.319 ° / Axial rise/subunit: 4.667 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 2814672
3D reconstructionResolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 460173 / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingB value: 66.05 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingDetails: ModelAngelo using sequence / Source name: Other / Type: in silico model

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