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- EMDB-50657: Helical reconstruction of human TIRAP -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-50657
TitleHelical reconstruction of human TIRAP
Map data
Sample
  • Complex: Helical Filament of TIRAP
    • Protein or peptide: Toll/interleukin-1 receptor domain-containing adapter protein
KeywordsFilament / TIR-domain / TLR-signalling / IMMUNE SYSTEM
Function / homology
Function and homology information


positive regulation of interleukin-15 production / TIRAP-dependent toll-like receptor 4 signaling pathway / cellular response to bacterial lipopeptide / regulation of interferon-beta production / positive regulation of toll-like receptor 3 signaling pathway / Toll-like receptor 4 binding / positive regulation of toll-like receptor 2 signaling pathway / Toll-like receptor 2 binding / positive regulation of chemokine (C-X-C motif) ligand 1 production / positive regulation of toll-like receptor 4 signaling pathway ...positive regulation of interleukin-15 production / TIRAP-dependent toll-like receptor 4 signaling pathway / cellular response to bacterial lipopeptide / regulation of interferon-beta production / positive regulation of toll-like receptor 3 signaling pathway / Toll-like receptor 4 binding / positive regulation of toll-like receptor 2 signaling pathway / Toll-like receptor 2 binding / positive regulation of chemokine (C-X-C motif) ligand 1 production / positive regulation of toll-like receptor 4 signaling pathway / myeloid cell differentiation / MyD88 deficiency (TLR2/4) / positive regulation of neutrophil chemotaxis / positive regulation of chemokine (C-X-C motif) ligand 2 production / extrinsic component of cytoplasmic side of plasma membrane / IRAK4 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / 3'-UTR-mediated mRNA stabilization / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / regulation of innate immune response / cellular response to lipoteichoic acid / endocytic vesicle / positive regulation of B cell proliferation / signaling adaptor activity / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of interleukin-12 production / protein kinase C binding / positive regulation of interleukin-8 production / positive regulation of JNK cascade / positive regulation of protein-containing complex assembly / positive regulation of interleukin-6 production / ruffle membrane / positive regulation of tumor necrosis factor production / ER-Phagosome pathway / protein-macromolecule adaptor activity / response to lipopolysaccharide / molecular adaptor activity / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-positive bacterium / inflammatory response / innate immune response / cell surface / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Toll-interleukin 1 receptor domain-containing adaptor protein, Tirap / TIR domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily
Similarity search - Domain/homology
Toll/interleukin-1 receptor domain-containing adapter protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSchaefer JH / Piehler J / Moeller A
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1557 Germany
CitationJournal: To Be Published
Title: Helical reconstruction of human TIRAP
Authors: Schaefer JH / Piehler J / Moeller A
History
DepositionJun 17, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50657.png

Downloads & links

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Map

FileDownload / File: emd_50657.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 300 pix.
= 277.2 Å		0.92 Å/pix.
x 300 pix.
= 277.2 Å		0.92 Å/pix.
x 300 pix.
= 277.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.924 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.271
Minimum - Maximum-1.1064181 - 2.1955225
Average (Standard dev.)0.0041974033 (±0.053483635)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 277.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50657_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50657_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_50657_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 : Helical Filament of TIRAP

EntireName: Helical Filament of TIRAP
Components
  • Complex: Helical Filament of TIRAP
    • Protein or peptide: Toll/interleukin-1 receptor domain-containing adapter protein

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Supramolecule #1: Helical Filament of TIRAP

SupramoleculeName: Helical Filament of TIRAP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Toll/interleukin-1 receptor domain-containing adapter protein

MacromoleculeName: Toll/interleukin-1 receptor domain-containing adapter protein
type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.738143 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGEQKLISE EDLSSGENLY FQGHMASSTS LPAPGSRPKK PLGKMADWFR QTLLKKPKKR PNSPESTSSD ASQPTSQDS PLPPSLSSVT SPSLPPTHAS DSGSSRWSKD YDVCVCHSEE DLVAAQDLVS YLEGSTASLR CFLQLRDATP G GAIVSELC ...String:
MGSSHHHHHH SSGEQKLISE EDLSSGENLY FQGHMASSTS LPAPGSRPKK PLGKMADWFR QTLLKKPKKR PNSPESTSSD ASQPTSQDS PLPPSLSSVT SPSLPPTHAS DSGSSRWSKD YDVCVCHSEE DLVAAQDLVS YLEGSTASLR CFLQLRDATP G GAIVSELC QALSSSHCRV LLITPGFLQD PWCKYQMLQA LTEAPGAEGC TIPLLSGLSR AAYPPELRFM YYVDGRGPDG GF RQVKEAV MRYLQTLS

UniProtKB: Toll/interleukin-1 receptor domain-containing adapter protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 16.6 Å
Applied symmetry - Helical parameters - Δ&Phi: -176 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 432673
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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