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- PDB-8z94: Cryo-EM structure of RIPK1 RHIM PFFs cross seeded RIPK3 RHIM amyl... -

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Basic information

Entry
Database: PDB / ID: 8z94
TitleCryo-EM structure of RIPK1 RHIM PFFs cross seeded RIPK3 RHIM amyloid fibril
ComponentsReceptor-interacting serine/threonine-protein kinase 3
KeywordsPROTEIN FIBRIL / amyloid fibril
Function / homology
Function and homology information


regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / regulation of activated T cell proliferation / regulation of adaptive immune response / Microbial modulation of RIPK1-mediated regulated necrosis / regulation of type II interferon production / TRIF-mediated programmed cell death / activation of protein kinase activity ...regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / regulation of activated T cell proliferation / regulation of adaptive immune response / Microbial modulation of RIPK1-mediated regulated necrosis / regulation of type II interferon production / TRIF-mediated programmed cell death / activation of protein kinase activity / TLR3-mediated TICAM1-dependent programmed cell death / programmed necrotic cell death / SARS-CoV-1-mediated effects on programmed cell death / necroptotic signaling pathway / RIP-mediated NFkB activation via ZBP1 / positive regulation of necroptotic process / non-canonical NF-kappaB signal transduction / RIPK1-mediated regulated necrosis / TRP channels / necroptotic process / T cell homeostasis / lymph node development / positive regulation of intrinsic apoptotic signaling pathway / spleen development / reactive oxygen species metabolic process / TICAM1, RIP1-mediated IKK complex recruitment / thymus development / IKK complex recruitment mediated by RIP1 / apoptotic signaling pathway / positive regulation of NF-kappaB transcription factor activity / protein modification process / Regulation of necroptotic cell death / cellular response to hydrogen peroxide / positive regulation of reactive oxygen species metabolic process / SARS-CoV-1 activates/modulates innate immune responses / T cell differentiation in thymus / regulation of apoptotic process / defense response to virus / amyloid fibril formation / transcription coactivator activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex binding / signal transduction / protein-containing complex / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
RHIM domain / RIP homotypic interaction motif / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...RHIM domain / RIP homotypic interaction motif / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Receptor-interacting serine/threonine-protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.56 Å
AuthorsMa, Y. / Zhao, K. / Liu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82188101 China
CitationJournal: To Be Published
Title: Cryo-EM structure of RIPK1 RHIM PFFs cross seeded RIPK3 RHIM amyloid fibril
Authors: Ma, Y. / Zhao, K. / Liu, C.
History
DepositionApr 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Apr 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Jul 23, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Receptor-interacting serine/threonine-protein kinase 3
A: Receptor-interacting serine/threonine-protein kinase 3
C: Receptor-interacting serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)45,9353
Polymers45,9353
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 3 / RIP-like protein kinase 3 / Receptor-interacting protein 3 / RIP-3


Mass: 15311.755 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RIPK3, RIP3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y572, 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: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: RIPK1 RHIM PFFs cross seeded human RIPK3 RHIM fibril / 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: 5
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: FEI TITAN 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 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -7.53 ° / Axial rise/subunit: 4.8 Å / Axial symmetry: C1
3D reconstructionResolution: 4.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45526 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.011513
ELECTRON MICROSCOPYf_angle_d1.42696
ELECTRON MICROSCOPYf_dihedral_angle_d11.704303
ELECTRON MICROSCOPYf_chiral_restr0.06681
ELECTRON MICROSCOPYf_plane_restr0.00890

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