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- EMDB-64870: Cryo-EM structure of human RIPK1 DD filament -

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Basic information

Entry
Database: EMDB / ID: EMD-64870
TitleCryo-EM structure of human RIPK1 DD filament
Map data
Sample
  • Organelle or cellular component: RIPK1 DD filament
    • Protein or peptide: Receptor-interacting serine/threonine-protein kinase 1
KeywordsDeath doamin / PROTEIN FIBRIL
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 / 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 / T cell apoptotic process / programmed necrotic cell death / Defective RIPK1-mediated regulated necrosis / Microbial modulation of RIPK1-mediated regulated necrosis / 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 / JUN kinase kinase kinase activity / negative regulation of necroptotic process / 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 / 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 / necroptotic process / 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 / canonical NF-kappaB signal transduction / 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 / TICAM1, RIP1-mediated IKK complex recruitment / protein serine/threonine kinase binding / IKK complex recruitment mediated by RIP1 / intrinsic apoptotic signaling pathway in response to DNA damage / TNFR1-induced NF-kappa-B signaling pathway / cellular response to tumor necrosis factor / Regulation of TNFR1 signaling / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to growth factor stimulus / positive regulation of JNK cascade / Regulation of necroptotic cell death / cellular response to hydrogen peroxide / positive regulation of reactive oxygen species metabolic process / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / Ovarian tumor domain proteases / positive regulation of neuron apoptotic process / response to oxidative stress / Potential therapeutics for SARS / amyloid fibril formation / positive regulation of canonical NF-kappaB signal transduction / protein kinase activity / non-specific serine/threonine protein kinase / signaling receptor complex / endosome membrane / intracellular signal transduction / Ub-specific processing proteases / positive regulation of apoptotic process / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression / ubiquitin protein ligase binding / apoptotic process / 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)
Methodhelical reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsZhao K / Liu JP / Liu C / Yuan JY
Funding support1 items
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, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64870.png

Downloads & links

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Map

FileDownload / File: emd_64870.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.059561886 - 0.118636414
Average (Standard dev.)0.00015924811 (±0.0032200322)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64870_msk_1.map
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Half map: #1

Fileemd_64870_half_map_1.map
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Half map: #2

Fileemd_64870_half_map_2.map
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Sample components

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Entire : RIPK1 DD filament

EntireName: RIPK1 DD filament
Components
  • Organelle or cellular component: RIPK1 DD filament
    • Protein or peptide: Receptor-interacting serine/threonine-protein kinase 1

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Supramolecule #1: RIPK1 DD filament

SupramoleculeName: RIPK1 DD filament / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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 / Details: GPGS is from vector / Number of copies: 20 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.141843 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPGSNTNFKE EPAAKYQAIF DNTTSLTDKH LDPIRENLGK HWKNCARKLG FTQSQIDEID HDYERDGLKE KVYQMLQKWV MREGIKGAT VGKLAQALHQ CSRIDLLSSL IYVSQN

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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.22311 Å
Applied symmetry - Helical parameters - Δ&Phi: 139.359 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 392912
CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ac5

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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