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- PDB-8rlm: TRIF Oligomerisation -

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Basic information

Entry
Database: PDB / ID: 8rlm
TitleTRIF Oligomerisation
ComponentsTIR domain-containing adapter molecule 1
KeywordsSIGNALING PROTEIN / TLR adaptor protein Helical filament TIR domain
Function / homology
Function and homology information


TICAM1 deficiency - HSE / TRAF3 deficiency - HSE / positive regulation of natural killer cell activation / MyD88-independent TLR4 cascade / Toll Like Receptor 3 (TLR3) Cascade / ripoptosome / cellular response to oxidised low-density lipoprotein particle stimulus / positive regulation of myeloid dendritic cell cytokine production / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death ...TICAM1 deficiency - HSE / TRAF3 deficiency - HSE / positive regulation of natural killer cell activation / MyD88-independent TLR4 cascade / Toll Like Receptor 3 (TLR3) Cascade / ripoptosome / cellular response to oxidised low-density lipoprotein particle stimulus / positive regulation of myeloid dendritic cell cytokine production / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / toll-like receptor 3 signaling pathway / Caspase activation via Death Receptors in the presence of ligand / TRIF-dependent toll-like receptor signaling pathway / RIP-mediated NFkB activation via ZBP1 / macrophage activation involved in immune response / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage cytokine production / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / response to exogenous dsRNA / B cell proliferation / regulation of protein-containing complex assembly / positive regulation of B cell proliferation / positive regulation of chemokine production / nitric oxide biosynthetic process / positive regulation of type I interferon production / signaling adaptor activity / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / positive regulation of autophagy / autophagosome / positive regulation of interferon-beta production / lipopolysaccharide-mediated signaling pathway / TRAF6-mediated induction of TAK1 complex within TLR4 complex / positive regulation of protein ubiquitination / TICAM1, RIP1-mediated IKK complex recruitment / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / apoptotic signaling pathway / positive regulation of interleukin-6 production / positive regulation of nitric oxide biosynthetic process / positive regulation of tumor necrosis factor production / cellular response to lipopolysaccharide / molecular adaptor activity / defense response to virus / early endosome / positive regulation of canonical NF-kappaB signal transduction / endosome membrane / endosome / inflammatory response / innate immune response / positive regulation of gene expression / protein kinase binding / mitochondrion / cytosol
Similarity search - Function
TIR domain-containing adapter molecule 1 / TRIF, N-terminal / TRIF N-terminal domain / : / RHIM domain / RIP homotypic interaction motif / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily
Similarity search - Domain/homology
TIR domain-containing adapter molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMoncrieffe, M.C. / Verstak, B. / Whitely, L. / Symmoms, M.F. / Soares, S.G. / Egelman, E.H. / Klenerman, D. / Bryant, C.E. / Gay, N.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Sci Adv / Year: 2026
Title: Toll-like receptor signaling outcome is determined by the stoichiometry of the endogenous TRIFosome.
Authors: Martin C Moncrieffe / Prasanna Suresh / Joe Boyle / Yuhao Cui / Bharti Nawalpuri / Brett Verstak / Yu P Zhang / Ziwei Zhang / Marcus Taylor / Edward H Egelman / Nicholas Gay / David Klenerman / Clare Bryant /
Abstract: Toll-like receptors (TLRs) drive innate immunity via assembly of macromolecular signal transduction platforms [supramolecular organizing centers (SMOCs)] coordinated by adaptor proteins such as ...Toll-like receptors (TLRs) drive innate immunity via assembly of macromolecular signal transduction platforms [supramolecular organizing centers (SMOCs)] coordinated by adaptor proteins such as Toll/interleukin-1 receptor (IL-1R) domain-containing adaptor-inducing interferon-β (TRIF), but whether oligomeric TRIFosomes form is unknown. Here, using cryo-electron microscopy and biophysical characterization of full-length TRIF in vitro, we show that it forms filamentous oligomers, which associate with the TRIF signaling partners receptor interacting protein 1 (RIP1) and RIP3 kinases, suggesting that oligomeric TRIFosomes could form. Endogenous TRIF, however, is predominantly monomeric in the absence of ligand, only forming TRIFosome oligomers in macrophages after stimulation of TLR4 or TLR3 when large, macromolecular signaling complexes form. TRIFosomes are fully formed 45 min after TLR3 or 60 min after TLR4 stimulation, commensurate with activation of nuclear factor κB in these cells. TLR3/4 activation triggers rapid interferon signaling prior to TRIFosome formation through monomeric TRIF, unexpectedly suggesting that a macromolecular platform of TRIF is not required to drive this signaling pathway. Collectively, these data show TRIFosome macromolecular platform formation and, unexpectedly, that TLR signaling can be SMOC-independent in addition to being SMOC-dependent.
History
DepositionJan 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TIR domain-containing adapter molecule 1
B: TIR domain-containing adapter molecule 1
C: TIR domain-containing adapter molecule 1
D: TIR domain-containing adapter molecule 1
E: TIR domain-containing adapter molecule 1
F: TIR domain-containing adapter molecule 1


Theoretical massNumber of molelcules
Total (without water)465,5516
Polymers465,5516
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
TIR domain-containing adapter molecule 1 / TICAM-1 / Proline-rich / vinculin and TIR domain-containing protein B / Putative NF-kappa-B- ...TICAM-1 / Proline-rich / vinculin and TIR domain-containing protein B / Putative NF-kappa-B-activating protein 502H / Toll-interleukin-1 receptor domain-containing adapter protein inducing interferon beta / MyD88-3 / TIR domain-containing adapter protein inducing IFN-beta


Mass: 77591.906 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TICAM1, PRVTIRB, TRIF / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8IUC6
Has protein modificationN

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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: TRIF TIR domain complex / Type: COMPLEX / Details: Full length TRIF / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 / Plasmid: pMCSG9
Buffer solutionpH: 8
Buffer component
IDConc.NameBuffer-ID
150 mMTRIS1
250 mMNaCl1
30.3 mMTCEP1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: 2600 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 1.15 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2cryoSPARC4image acquisition
4cryoSPARC4CTF correction
7MOLREPmodel fitting
12cryoSPARC43D reconstruction
13PHENIX(1.21rc1_5081model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 178.3 ° / Axial rise/subunit: 16.1 Å / Axial symmetry: C1
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 500264 / Symmetry type: HELICAL
Atomic model buildingB value: 88 / Protocol: AB INITIO MODEL / Space: REAL
Atomic model buildingAccession code: AF-Q8IUC6 / Source name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027566
ELECTRON MICROSCOPYf_angle_d0.57410212
ELECTRON MICROSCOPYf_dihedral_angle_d3.9531008
ELECTRON MICROSCOPYf_chiral_restr0.0371146
ELECTRON MICROSCOPYf_plane_restr0.0061350

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