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- EMDB-67084: RIPK1 death domain filamentation drives TNF-induced apoptosis -

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Basic information

Entry
Database: EMDB / ID: EMD-67084
TitleRIPK1 death domain filamentation drives TNF-induced apoptosis
Map data
Sample
  • Complex: RIPK1 death domain filament
    • Protein or peptide: Receptor-interacting serine/threonine-protein kinase 1
Keywordspro-inflammatory pathway / cell death / IMMUNE SYSTEM / APOPTOSIS
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 / T cell apoptotic process / programmed necrotic cell death / Defective RIPK1-mediated regulated necrosis / Microbial modulation of RIPK1-mediated regulated necrosis / tumor necrosis factor receptor superfamily complex ...ripoptosome assembly / positive regulation of miRNA processing / positive regulation of interleukin-6-mediated signaling pathway / death domain binding / ripoptosome assembly involved in necroptotic process / T cell apoptotic process / programmed necrotic cell death / Defective RIPK1-mediated regulated necrosis / Microbial modulation of RIPK1-mediated regulated necrosis / tumor necrosis factor receptor superfamily complex / TRIF-mediated programmed cell death / ripoptosome / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TLR3-mediated TICAM1-dependent programmed cell death / activation of protein kinase activity / positive regulation of macrophage differentiation / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / SARS-CoV-1-mediated effects on programmed cell death / necroptotic process / JUN kinase kinase kinase activity / necroptotic signaling pathway / negative regulation of necroptotic process / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / death-inducing signaling complex / RIP-mediated NFkB activation via ZBP1 / positive regulation of necroptotic process / Dengue virus modulates apoptosis / 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 / TNFR1-induced proapoptotic signaling / positive regulation of programmed cell death / RIPK1-mediated regulated necrosis / extrinsic apoptotic signaling pathway via death domain receptors / TRP channels / protein serine/threonine phosphatase activity / response to tumor necrosis factor / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of execution phase of apoptosis / extrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / signaling adaptor activity / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of interleukin-8 production / negative regulation of canonical NF-kappaB signal transduction / canonical NF-kappaB signal transduction / TICAM1, RIP1-mediated IKK complex recruitment / protein serine/threonine kinase binding / cellular response to tumor necrosis factor / IKK complex recruitment mediated by RIP1 / intrinsic apoptotic signaling pathway in response to DNA damage / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of JNK cascade / cellular response to growth factor stimulus / Regulation of necroptotic cell death / positive regulation of reactive oxygen species metabolic process / positive regulation of neuron apoptotic process / positive regulation of inflammatory response / cellular response to hydrogen peroxide / positive regulation of tumor necrosis factor production / Ovarian tumor domain proteases / response to oxidative stress / amyloid fibril formation / Potential therapeutics for SARS / apoptotic process / inflammatory response / protein kinase activity / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / signaling receptor complex / intracellular signal transduction / Ub-specific processing proteases / endosome membrane / positive regulation of apoptotic process / protein serine kinase activity / ubiquitin protein ligase binding / protein serine/threonine kinase activity / 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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsLiu P / Tan YB / Luo D
Funding support Singapore, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-CRP26-2021-0001 Singapore
CitationJournal: To Be Published
Title: RIPK1 Death Domain Filamentation Drives TNF-Induced Apoptosis
Authors: Chen Y / Liu P / Tan YB / Luo D / Tergaonkar V
History
DepositionNov 14, 2025-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_67084.png

Downloads & links

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Map

FileDownload / File: emd_67084.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 400 pix.
= 302.8 Å		0.76 Å/pix.
x 400 pix.
= 302.8 Å		0.76 Å/pix.
x 400 pix.
= 302.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.757 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0409
Minimum - Maximum-0.13285077 - 0.31581277
Average (Standard dev.)0.000024110795 (±0.012267205)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 302.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_67084_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67084_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RIPK1 death domain filament

EntireName: RIPK1 death domain filament
Components
  • Complex: RIPK1 death domain filament
    • Protein or peptide: Receptor-interacting serine/threonine-protein kinase 1

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Supramolecule #1: RIPK1 death domain filament

SupramoleculeName: RIPK1 death domain filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.8 kDa/nm

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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: 25 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.843546 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
NTNFKEEPAA KYQAIFDNTT SLTDKHLDPI RENLGKHWKN CARKLGFTQS QIDEIDHDYE RDGLKEKVYQ MLQKWVMREG IKGATVGKL AQALHQCSRI DLLSSLIYVS QN

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.7 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMHEPESHEPES
150.0 mMNaClsodium chloride

Details: 25mM HEPES, 150mM NaCl
GridModel: Quantifoil / Material: NICKEL / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK III
DetailsThe sample forms filament.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionDetails: template picker and filament tracer
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ModelAngelo generated backbone PDB model.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 347692
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Details: Ab-initio reconstructions, power spectra search, heterogenous refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Software - details: helical refinement / Details: helical refinement
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC / Details: heterogenous refinement

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9xon:
RIPK1 death domain filamentation drives TNF-induced apoptosis

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