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- PDB-9v9e: Cryo-EM structure of human RIPK1 DD filament -

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Basic information

Entry
Database: PDB / ID: 9v9e
TitleCryo-EM structure of human RIPK1 DD filament
ComponentsReceptor-interacting serine/threonine-protein kinase 1
KeywordsPROTEIN FIBRIL / Death doamin
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 / peptidyl-serine autophosphorylation / 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 / peptidyl-serine autophosphorylation / 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 / programmed necrotic cell death / TNF signaling / SARS-CoV-1-mediated effects on programmed cell death / Caspase activation via Death Receptors in the presence of ligand / T cell apoptotic process / positive regulation of macrophage differentiation / JUN kinase kinase kinase activity / necroptotic signaling pathway / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / RIP-mediated NFkB activation via ZBP1 / 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 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 / TRP channels / necroptotic process / 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 / canonical NF-kappaB signal transduction / signaling adaptor activity / TICAM1, RIP1-mediated IKK complex recruitment / tumor necrosis factor-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / : / positive regulation of interleukin-8 production / IKK complex recruitment mediated by RIP1 / protein catabolic process / protein serine/threonine kinase binding / TNFR1-induced NF-kappa-B signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Regulation of TNFR1 signaling / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein phosphorylation / positive regulation of JNK cascade / Regulation of necroptotic cell death / cellular response to growth factor stimulus / cellular response to tumor necrosis factor / positive regulation of reactive oxygen species metabolic process / cellular response to hydrogen peroxide / positive regulation of tumor necrosis factor production / positive regulation of inflammatory response / Ovarian tumor domain proteases / protein autophosphorylation / positive regulation of neuron apoptotic process / response to oxidative stress / amyloid fibril formation / Potential therapeutics for SARS / protein kinase activity / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / signaling receptor complex / endosome membrane / Ub-specific processing proteases / 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 / positive regulation of gene expression / 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 / cytoplasm / cytosol
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: 2.87 Å
AuthorsZhao, K. / Liu, J.P. / Liu, C. / Yuan, J.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2026
Title: Electric dipole moment drives the dynamics of the TNFR1 complex I signalosome.
Authors: Jianping Liu / Jing Zhao / Jiayang Gao / Kun Zhao / Yaoyao Han / Jing Yang / Zefei Li / Jianyu Ye / Ziyu Sun / Fengyi Wang / Xinyi Liu / Zekai Li / Siyu Ji / Bo Liu / Cong Liu / Yixiao Zhang ...Authors: Jianping Liu / Jing Zhao / Jiayang Gao / Kun Zhao / Yaoyao Han / Jing Yang / Zefei Li / Jianyu Ye / Ziyu Sun / Fengyi Wang / Xinyi Liu / Zekai Li / Siyu Ji / Bo Liu / Cong Liu / Yixiao Zhang / Junying Yuan / James J Chou /
Abstract: Dynamic assembly of the complex I signalosome mediated by three death domain (DD)-containing proteins-TNFR1, TRADD and RIPK1-is key for transmitting extracellular TNF stimuli to intracellular NF-κB ...Dynamic assembly of the complex I signalosome mediated by three death domain (DD)-containing proteins-TNFR1, TRADD and RIPK1-is key for transmitting extracellular TNF stimuli to intracellular NF-κB signalling in controlling 'live or die' cell fate. This signalling hub features the rapid recruitment of TRADD and RIPK1 after engagement of TNFR1 by TNF for the formation of complex I, followed by timed disassembly for transition into downstream signalling complexes, but the mechanism driving the dynamic reversibility of complex I remains unclear. Here we captured the assembly core of complex I and determined its cryo-electron microscopy structure, showing a pentameric fibre comprising 31 DDs, with a single layer of a TRADD-DD pentamer sandwiched between multiple layers of TNFR1-DD and RIPK1-DD homopentamers. Structural analysis revealed a strong opposing electric dipole moment (EDM) generated by RIPK1-DD oligomerization relative to that of TNFR1-DD and TRADD-DD. Structure-guided mutagenesis in TNFR1-TRADD-RIPK1 pentameric fibres altering the EDM without affecting DD oligomerization demonstrated the role and mechanism of EDM in driving the dynamic reversibility mediating the rapid assembly and disassembly of complex I. Our study demonstrates a role for long-range interactions mediated by protein EDMs in driving the assembly and disassembly of super-signalling complex I for promoting NF-κB signalling.
History
DepositionMay 30, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
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Revision 1.1Apr 15, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / EM metadata / EM metadata
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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


Theoretical massNumber of molelcules
Total (without water)262,83720
Polymers262,83720
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: 13141.843 Da / Num. of mol.: 20 / Fragment: RIPK1 death domain
Source method: isolated from a genetically manipulated source
Details: GPGS is from vector / Source: (gene. exp.) Homo sapiens (human) / Gene: RIPK1, RIP, RIP1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13546, non-specific serine/threonine protein kinase
Has protein modificationY

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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: RIPK1 DD filament / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2300 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.15.2_3472 / Category: model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 139.359 ° / Axial rise/subunit: 5.22311 Å / Axial symmetry: C1
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 392912 / Symmetry type: HELICAL
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00316660
ELECTRON MICROSCOPYf_angle_d0.46522400
ELECTRON MICROSCOPYf_dihedral_angle_d1.80214280
ELECTRON MICROSCOPYf_chiral_restr0.0372440
ELECTRON MICROSCOPYf_plane_restr0.0022840

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