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- EMDB-52356: cryoEM structure of amyloid fibrils formed by human RIPK1 -

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Basic information

Entry
Database: EMDB / ID: EMD-52356
TitlecryoEM structure of amyloid fibrils formed by human RIPK1
Map data
Sample
  • Complex: hRIPK1 RHIM-mediated amyloid fibril
    • Protein or peptide: Receptor-interacting serine/threonine-protein kinase 1
KeywordsAmyloid / kinase / PROTEIN FIBRIL
Function / homology
Function and homology information


ripoptosome assembly / positive regulation of miRNA processing / positive regulation of interleukin-6-mediated signaling pathway / ripoptosome assembly involved in necroptotic process / death domain binding / peptidyl-serine autophosphorylation / ripoptosome / 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 / ripoptosome assembly involved in necroptotic process / death domain binding / peptidyl-serine autophosphorylation / ripoptosome / Defective RIPK1-mediated regulated necrosis / Microbial modulation of RIPK1-mediated regulated necrosis / 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 / Caspase activation via Death Receptors in the presence of ligand / SARS-CoV-1-mediated effects on programmed cell death / positive regulation of macrophage differentiation / T cell apoptotic process / JUN kinase kinase kinase activity / necroptotic signaling pathway / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / death-inducing signaling complex / positive regulation of necroptotic process / RIP-mediated NFkB activation via ZBP1 / 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 / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / TRP channels / necroptotic process / response to tumor necrosis factor / positive regulation of execution phase of apoptosis / canonical NF-kappaB signal transduction / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway / TICAM1, RIP1-mediated IKK complex recruitment / signaling adaptor activity / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Regulation of TNFR1 signaling / tumor necrosis factor-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of interleukin-8 production / positive regulation of JNK cascade / Regulation of necroptotic cell death / protein catabolic process / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / cellular response to growth factor stimulus / cellular response to hydrogen peroxide / Ovarian tumor domain proteases / positive regulation of protein phosphorylation / positive regulation of reactive oxygen species metabolic process / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / positive regulation of neuron apoptotic process / protein autophosphorylation / response to oxidative stress / amyloid fibril formation / Potential therapeutics for SARS / endosome membrane / receptor complex / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / Ub-specific processing proteases / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / apoptotic process / 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 / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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: 2.57 Å
AuthorsLopez-Alonso JP / Ubarretxena-Belandia I / Jian H
Funding support Spain, 1 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: To Be Published
Title: Molecular Structure of Human Receptor Interacting Protein Kinase 1 (RIPK1) in its Fibrillar Conformation Elucidated by Solid-State NMR and Cryo-Electron Microscopy
Authors: Polonio P / Lopez-Alonso JP / Ubarretxena-Belandia I / Jiang H / Escobedo-Gonzales FC / Titaux-Delgado GA / Mompean M
History
DepositionDec 17, 2024-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52356.png

Downloads & links

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Map

FileDownload / File: emd_52356.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.51 Å/pix.
x 640 pix.
= 323.456 Å		0.51 Å/pix.
x 640 pix.
= 323.456 Å		0.51 Å/pix.
x 640 pix.
= 323.456 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.5054 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0155
Minimum - Maximum-0.09499223 - 0.17951898
Average (Standard dev.)0.00013057729 (±0.0035335084)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 323.456 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52356_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52356_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52356_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : hRIPK1 RHIM-mediated amyloid fibril

EntireName: hRIPK1 RHIM-mediated amyloid fibril
Components
  • Complex: hRIPK1 RHIM-mediated amyloid fibril
    • Protein or peptide: Receptor-interacting serine/threonine-protein kinase 1

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Supramolecule #1: hRIPK1 RHIM-mediated amyloid fibril

SupramoleculeName: hRIPK1 RHIM-mediated amyloid fibril / type: complex / 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 / Number of copies: 5 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.656604 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
HMPSLHNIPV PETNYLGNTP TMPFSSLPPT DESIKYTIYN STGIQIGAYN YMEIGGTSSS LLDSTNTNFK EEPAAKYQAI FDNTTSLT

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 statehelical array

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Sample preparation

Concentration0.765 mg/mL
BufferpH: 7.5 / Component - Concentration: 50.0 mM / Component - Name: TrisHCl
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Pressure: 0.00035 kPa / Details: 9 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: time 5.5s, blotting force 2.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Average exposure time: 0.88 sec. / Average electron dose: 49.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 4.667 Å
Applied symmetry - Helical parameters - Δ&Phi: -7.319 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 460173
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 2814672 / Software - Name: cryoSPARC (ver. 4.6.0)
Startup modelType of model: INSILICO MODEL / In silico model: ab initio model
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo using sequence
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 66.05
Output model

PDB-9hr6:
cryoEM structure of amyloid fibrils formed by human RIPK1

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