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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 / ripoptosome / MyD88-independent TLR4 cascade / Toll Like Receptor 3 (TLR3) Cascade / TRIF-mediated programmed cell death / positive regulation of myeloid dendritic cell cytokine production / cellular response to oxidised low-density lipoprotein particle stimulus / TLR3-mediated TICAM1-dependent programmed cell death ...TICAM1 deficiency - HSE / TRAF3 deficiency - HSE / positive regulation of natural killer cell activation / ripoptosome / MyD88-independent TLR4 cascade / Toll Like Receptor 3 (TLR3) Cascade / TRIF-mediated programmed cell death / positive regulation of myeloid dendritic cell cytokine production / cellular response to oxidised low-density lipoprotein particle stimulus / TLR3-mediated TICAM1-dependent programmed cell death / Caspase activation via Death Receptors in the presence of ligand / toll-like receptor 3 signaling pathway / 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 / positive regulation of type I interferon production / regulation of protein-containing complex assembly / positive regulation of chemokine production / positive regulation of B cell proliferation / signaling adaptor activity / nitric oxide biosynthetic process / positive regulation of autophagy / 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 / TRAF6-mediated induction of TAK1 complex within TLR4 complex / autophagosome / positive regulation of interferon-beta production / lipopolysaccharide-mediated signaling pathway / TICAM1, RIP1-mediated IKK complex recruitment / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / 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 / defense response to virus / molecular adaptor activity / early endosome / positive regulation of canonical NF-kappaB signal transduction / endosome / endosome membrane / 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: To Be Published
Title: TRIF Oligomerisation Determines Signalosome Architecture in Toll-like Receptor Signalling
Authors: Moncrieffe, M.C. / Verstak, B. / Whitely, L. / Simmons, M.F. / Soares, S.G. / Edelman, E.H. / Klenerman, D. / Bryant, C.E. / Gay, N.J.
History
DepositionJan 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data 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: 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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