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

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Basic information

Entry
Database: PDB / ID: 9xon
TitleRIPK1 death domain filamentation drives TNF-induced apoptosis
ComponentsReceptor-interacting serine/threonine-protein kinase 1
KeywordsAPOPTOSIS / pro-inflammatory pathway / cell death / IMMUNE SYSTEM
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsLiu, P. / Tan, Y.B. / Luo, D.
Funding support Singapore, 1items
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, Y.B. / Luo, D. / Tergaonkar, V.
History
DepositionNov 14, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
F: 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
L: Receptor-interacting serine/threonine-protein kinase 1
M: Receptor-interacting serine/threonine-protein kinase 1
N: Receptor-interacting serine/threonine-protein kinase 1
O: Receptor-interacting serine/threonine-protein kinase 1
P: Receptor-interacting serine/threonine-protein kinase 1
Q: Receptor-interacting serine/threonine-protein kinase 1
R: Receptor-interacting serine/threonine-protein kinase 1
S: Receptor-interacting serine/threonine-protein kinase 1
T: Receptor-interacting serine/threonine-protein kinase 1
U: Receptor-interacting serine/threonine-protein kinase 1
V: Receptor-interacting serine/threonine-protein kinase 1
W: Receptor-interacting serine/threonine-protein kinase 1
X: Receptor-interacting serine/threonine-protein kinase 1
Y: Receptor-interacting serine/threonine-protein kinase 1


Theoretical massNumber of molelcules
Total (without water)321,08925
Polymers321,08925
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 / Serine/threonine-protein kinase RIP


Mass: 12843.546 Da / Num. of mol.: 25
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RIPK1, RIP, RIP1 / 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: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RIPK1 death domain filament / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 12.8 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 25mM HEPES, 150mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESHEPES1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample forms filament.
Specimen supportGrid material: NICKEL / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K

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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: 1600 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARCparticle selection
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignmenthelical refinement
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIX1.20.1_4487model refinement
14Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionDetails: template picker and filament tracer
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 347692 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: in silico model
RefinementHighest resolution: 2.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00420950
ELECTRON MICROSCOPYf_angle_d0.60128150
ELECTRON MICROSCOPYf_dihedral_angle_d5.1442750
ELECTRON MICROSCOPYf_chiral_restr0.0423050
ELECTRON MICROSCOPYf_plane_restr0.0043600

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