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- EMDB-62587: Cryo-EM structure of mouse RIPK1-DD filament -

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Basic information

Entry
Database: EMDB / ID: EMD-62587
TitleCryo-EM structure of mouse RIPK1-DD filament
Map data
Sample
  • Complex: Receptor-interacting serine/threonine-protein kinase 1
    • Protein or peptide: Receptor-interacting serine/threonine-protein kinase 1
KeywordsRIPK1 / death domain / 568-656 / dimerization / IMMUNE SYSTEM
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 / ripoptosome assembly involved in necroptotic process / TNFR1-induced NF-kappa-B signaling pathway / death domain binding / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / Ovarian tumor domain proteases / IKK complex recruitment mediated by RIP1 / peptidyl-serine autophosphorylation / ripoptosome / programmed necrotic cell death / positive regulation of macrophage differentiation / T cell apoptotic process / TRP channels / necroptotic signaling pathway / Ub-specific processing proteases / death-inducing signaling complex / positive regulation of necroptotic process / negative regulation of necroptotic process / positive regulation of tumor necrosis factor-mediated signaling pathway / death receptor binding / positive regulation of extrinsic apoptotic signaling pathway / regulation of reactive oxygen species metabolic process / necroptotic process / positive regulation of phosphorylation / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of execution phase of apoptosis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / signaling adaptor activity / negative regulation of canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of interleukin-8 production / positive regulation of JNK cascade / protein catabolic process / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / cellular response to growth factor stimulus / cellular response to hydrogen peroxide / positive regulation of protein phosphorylation / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / positive regulation of neuron apoptotic process / protein autophosphorylation / amyloid fibril formation / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / receptor complex / protein kinase activity / positive regulation of MAPK cascade / intracellular signal transduction / positive regulation of apoptotic process / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein-containing complex binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / ATP binding
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 / Serine-threonine/tyrosine-protein kinase, catalytic domain ...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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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)
Methodhelical reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsZhang H
Funding support China, 2 items
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, 2024-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62587.png

Downloads & links

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Map

FileDownload / File: emd_62587.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 422. Å		1.06 Å/pix.
x 400 pix.
= 422. Å		1.06 Å/pix.
x 400 pix.
= 422. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.4571859 - 0.704092
Average (Standard dev.)0.00051158346 (±0.016750861)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 421.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62587_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_62587_half_map_2.map
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Sample components

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Entire : Receptor-interacting serine/threonine-protein kinase 1

EntireName: Receptor-interacting serine/threonine-protein kinase 1
Components
  • Complex: Receptor-interacting serine/threonine-protein kinase 1
    • Protein or peptide: Receptor-interacting serine/threonine-protein kinase 1

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Supramolecule #1: Receptor-interacting serine/threonine-protein kinase 1

SupramoleculeName: Receptor-interacting serine/threonine-protein kinase 1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 1.017 KDa

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Macromolecule #1: Receptor-interacting serine/threonine-protein kinase 1

MacromoleculeName: Receptor-interacting serine/threonine-protein kinase 1
type: protein_or_peptide / ID: 1 / Number of copies: 23 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.81067 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGSSHHHHHH SSGLVPRGSH MLEVLFQGPV DTDEHLNPIR ENLGRQWKNC ARKLGFTESQ IDEIDHDYER DGLKEKVYQM LQKWLMREG TKGATVGKLA QALHQCCRID LLNHLIRASQ S

UniProtKB: Receptor-interacting serine/threonine-protein kinase 1

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.41 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.96 Å
Applied symmetry - Helical parameters - Δ&Phi: 139.82 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 988646
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE

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