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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 / TNF signaling / programmed necrotic cell death / 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 / positive regulation of execution phase of apoptosis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway / canonical NF-kappaB signal transduction / signaling adaptor activity / TICAM1, RIP1-mediated IKK complex recruitment / tumor necrosis factor-mediated signaling pathway / : / IKK complex recruitment mediated by RIP1 / negative regulation of extrinsic apoptotic signaling pathway / protein serine/threonine kinase binding / positive regulation of interleukin-8 production / protein catabolic process / 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 / positive regulation of canonical NF-kappaB signal transduction / protein kinase activity / 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: Zhao, K. / Liu, J.P. / Liu, C. / Yuan, J.Y.
History
DepositionMay 30, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / 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


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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