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- EMDB-19341: TRIF Oligomerisation -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-19341
TitleTRIF Oligomerisation
Map data
Sample
  • Complex: TRIF TIR domain complex
    • Protein or peptide: TIR domain-containing adapter molecule 1
KeywordsTLR adaptor protein Helical filament TIR domain / SIGNALING PROTEIN
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 / cellular response to oxidised low-density lipoprotein particle stimulus / TLR3-mediated TICAM1-dependent programmed cell death / positive regulation of myeloid dendritic cell cytokine production ...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 / cellular response to oxidised low-density lipoprotein particle stimulus / TLR3-mediated TICAM1-dependent programmed cell death / positive regulation of myeloid dendritic cell cytokine production / 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 tumor necrosis factor production / positive regulation of nitric oxide biosynthetic process / cellular response to lipopolysaccharide / molecular adaptor activity / defense response to virus / 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)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMoncrieffe MC / Verstak B / Whitely L / Symmoms MF / Soares SG / Egelman EH / Klenerman D / Bryant CE / Gay NJ
Funding support United Kingdom, 1 items
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 MC / Verstak B / Whitely L / Simmons MF / Soares SG / Edelman EH / Klenerman D / Bryant CE / Gay NJ
History
DepositionJan 3, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19341.png

Downloads & links

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Map

FileDownload / File: emd_19341.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 216 pix.
= 230.256 Å		1.07 Å/pix.
x 216 pix.
= 230.256 Å		1.07 Å/pix.
x 216 pix.
= 230.256 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.066 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.54767764 - 0.9892771
Average (Standard dev.)0.0018270701 (±0.028186986)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 230.256 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19341_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19341_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TRIF TIR domain complex

EntireName: TRIF TIR domain complex
Components
  • Complex: TRIF TIR domain complex
    • Protein or peptide: TIR domain-containing adapter molecule 1

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Supramolecule #1: TRIF TIR domain complex

SupramoleculeName: TRIF TIR domain complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Full length TRIF
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: TIR domain-containing adapter molecule 1

MacromoleculeName: TIR domain-containing adapter molecule 1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.591906 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: SNAMACTGPS LPSAFDILGA AGQDKLLYLK HKLKTPRPGC QGQDLLHAMV LLKLGQETEA RISLEALKAD AVARLVARQW AGVDSTEDP EEPPDVSWAV ARLYHLLAEE KLCPASLRDV AYQEAVRTLS SRDDHRLGEL QDEARNRCGW DIAGDPGSIR T LQSNLGCL ...String:
SNAMACTGPS LPSAFDILGA AGQDKLLYLK HKLKTPRPGC QGQDLLHAMV LLKLGQETEA RISLEALKAD AVARLVARQW AGVDSTEDP EEPPDVSWAV ARLYHLLAEE KLCPASLRDV AYQEAVRTLS SRDDHRLGEL QDEARNRCGW DIAGDPGSIR T LQSNLGCL PPSSALPSGT RSLPRPIDGV SDWSQGCSLR STGSPASLAS NLEISQSPTM PFLSLHRSPH GPSKLCDDPQ AS LVPEPVP GGCQEPEEMS WPPSGEIASP PELPSSPPPG LPEVAPDATS TGLPDTPAAP ETSTNYPVEC TEGSAGPQSL PLP ILEPVE NPCSVKDQTP LQLSVEDTTS PNTKPCPPTP TTPETSPPPP PPPPSSTPCS AHLTPSSLFP SSLESSSEQK FYNF VILHA RADEHIALRV REKLEALGVP DGATFCEDFQ VPGRGELSCL QDAIDHSAFI ILLLTSNFDC RLSLHQVNQA MMSNL TRQG SPDCVIPFLP LESSPAQLSS DTASLLSGLV RLDEHSQIFA RKVANTFKPH RLQARKAMWR KEQDTRALRE QSQHLD GER MQAAALNAAY SAYLQSYLSY QAQMEQLQVA FGSHMSFGTG APYGARMPFG GQVPLGAPPP FPTWPGCPQP PPLHAWQ AG TPPPPSPQPA AFPQSLPFPQ SPAFPTASPA PPQSPGLQPL IIHHAQMVQL GLNNHMWNQR GSQAPEDKTQ EAEHHHHH H

UniProtKB: TIR domain-containing adapter molecule 1

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 8
Component:
ConcentrationName
50.0 mMTRIS
50.0 mMNaCl
0.3 mMTCEP
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.15 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 16.1 Å
Applied symmetry - Helical parameters - Δ&Phi: 178.3 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 500264
CTF correctionSoftware - Name: cryoSPARC (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AlphaFold
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

iuc6


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 88
Output model

PDB-8rlm:
TRIF Oligomerisation

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