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- PDB-9kv7: Cryo-EM structure of mouse RIPK1-DD filament -

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Basic information

Entry
Database: PDB / ID: 9kv7
TitleCryo-EM structure of mouse RIPK1-DD filament
ComponentsReceptor-interacting serine/threonine-protein kinase 1
KeywordsIMMUNE SYSTEM / RIPK1 / death domain / 568-656 / dimerization
Function / homology
Function and homology information


TNF signaling / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TNFR1-induced proapoptotic signaling / Caspase activation via Death Receptors in the presence of ligand / RIPK1-mediated regulated necrosis / TRIF-mediated programmed cell death / ripoptosome assembly / positive regulation of miRNA processing ...TNF signaling / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TNFR1-induced proapoptotic signaling / Caspase activation via Death Receptors in the presence of ligand / RIPK1-mediated regulated necrosis / TRIF-mediated programmed cell death / ripoptosome assembly / positive regulation of miRNA processing / positive regulation of interleukin-6-mediated signaling pathway / death domain binding / peptidyl-serine autophosphorylation / TNFR1-induced NF-kappa-B signaling pathway / ripoptosome assembly involved in necroptotic process / Regulation of necroptotic cell death / Ovarian tumor domain proteases / Regulation of TNFR1 signaling / T cell apoptotic process / IKK complex recruitment mediated by RIP1 / programmed necrotic cell death / ripoptosome / activation of protein kinase activity / positive regulation of macrophage differentiation / necroptotic process / negative regulation of necroptotic process / JUN kinase kinase kinase activity / necroptotic signaling pathway / TRP channels / death-inducing signaling complex / Ub-specific processing proteases / positive regulation of necroptotic process / positive regulation of tumor necrosis factor-mediated signaling pathway / death receptor binding / positive regulation of programmed necrotic cell death / positive regulation of extrinsic apoptotic signaling pathway / regulation of reactive oxygen species metabolic process / positive regulation of programmed cell death / extrinsic apoptotic signaling pathway via death domain receptors / protein serine/threonine phosphatase activity / response to tumor necrosis factor / positive regulation of phosphorylation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of execution phase of apoptosis / extrinsic apoptotic signaling pathway / canonical NF-kappaB signal transduction / protein catabolic process / signaling adaptor activity / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-8 production / protein serine/threonine kinase binding / cellular response to tumor necrosis factor / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to growth factor stimulus / positive regulation of protein phosphorylation / positive regulation of JNK cascade / cellular response to hydrogen peroxide / positive regulation of inflammatory response / positive regulation of neuron apoptotic process / positive regulation of tumor necrosis factor production / protein autophosphorylation / response to oxidative stress / amyloid fibril formation / positive regulation of MAPK cascade / positive regulation of canonical NF-kappaB signal transduction / protein kinase activity / non-specific serine/threonine protein kinase / signaling receptor complex / intracellular signal transduction / positive regulation of apoptotic process / inflammatory response / protein serine kinase activity / ubiquitin protein ligase binding / protein serine/threonine kinase activity / apoptotic process / positive regulation of gene expression / negative regulation of apoptotic process / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / mitochondrion / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
RIP1, Death domain / RHIM domain / RIP homotypic interaction motif / 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 ...RIP1, Death domain / RHIM domain / RIP homotypic interaction motif / 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 speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsZhang, H.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Metab / Year: 2025
Title: RIPK1 senses S-adenosylmethionine scarcity to drive cell death and inflammation.
Authors: Zezhao Chen / Xiaosong Gu / Hongbo Chen / Huijing Zhang / Jianping Liu / Xiaohua Yang / Yuping Cai / Mengmeng Zhang / Lingjie Yan / Yuanxin Yang / Bing Shan / Zheng-Jiang Zhu / Yixiao Zhang ...Authors: Zezhao Chen / Xiaosong Gu / Hongbo Chen / Huijing Zhang / Jianping Liu / Xiaohua Yang / Yuping Cai / Mengmeng Zhang / Lingjie Yan / Yuanxin Yang / Bing Shan / Zheng-Jiang Zhu / Yixiao Zhang / Jinyang Gu / Daichao Xu /
Abstract: The capacity of cells to sense and respond to nutrient availability is essential for metabolic homeostasis. Failure in this process may cause cell death and associated diseases. While nutrient ...The capacity of cells to sense and respond to nutrient availability is essential for metabolic homeostasis. Failure in this process may cause cell death and associated diseases. While nutrient sensing in metabolic pathways is well understood, the mechanisms linking nutrient signals to cell death remain unclear. Here, we show that RIPK1, a key mediator of cell death and inflammation, senses methionine and its metabolite, S-adenosylmethionine (SAM), to dictate cell survival and death. SAM-mediated symmetrical dimethylation at RIPK1 Arg606 by PRMT5 functions as a physiological protective brake against RIPK1 activation. Metabolic perturbations, such as methionine restriction or disrupted one-carbon flux, reduce SAM levels and unmask Arg606, promoting RIPK1 self-association and trans-activation, thereby triggering apoptosis and inflammation. Thus, RIPK1 is a physiological SAM sensor linking methionine and one-carbon metabolism to the control of life-or-death decisions. Our findings suggest that RIPK1 could be a potential target for diseases associated with disrupted SAM availability.
History
DepositionDec 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 15, 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
G: Receptor-interacting serine/threonine-protein kinase 1
H: Receptor-interacting serine/threonine-protein kinase 1
I: Receptor-interacting serine/threonine-protein kinase 1
J: Receptor-interacting serine/threonine-protein kinase 1
K: 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
F: Receptor-interacting serine/threonine-protein kinase 1
L: Receptor-interacting serine/threonine-protein kinase 1
P: Receptor-interacting serine/threonine-protein kinase 1
R: Receptor-interacting serine/threonine-protein kinase 1
V: Receptor-interacting serine/threonine-protein kinase 1
X: Receptor-interacting serine/threonine-protein kinase 1
M: Receptor-interacting serine/threonine-protein kinase 1
Q: Receptor-interacting serine/threonine-protein kinase 1
S: Receptor-interacting serine/threonine-protein kinase 1
U: Receptor-interacting serine/threonine-protein kinase 1
W: Receptor-interacting serine/threonine-protein kinase 1
N: Receptor-interacting serine/threonine-protein kinase 1
O: Receptor-interacting serine/threonine-protein kinase 1


Theoretical massNumber of molelcules
Total (without water)317,64523
Polymers317,64523
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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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: 13810.670 Da / Num. of mol.: 23
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ripk1, Rinp, Rip / Production host: Escherichia coli (E. coli)
References: UniProt: Q60855, 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: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Receptor-interacting serine/threonine-protein kinase 1
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.001017 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 49.41 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 139.82 ° / Axial rise/subunit: 4.96 Å / Axial symmetry: C1
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 988646 / Symmetry type: HELICAL
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00516629
ELECTRON MICROSCOPYf_angle_d0.56422287
ELECTRON MICROSCOPYf_dihedral_angle_d4.0872185
ELECTRON MICROSCOPYf_chiral_restr0.042369
ELECTRON MICROSCOPYf_plane_restr0.0032898

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