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- EMDB-39676: Cryo-EM structure of cylindrical fiber of MyD88 TIR -

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Basic information

Entry
Database: EMDB / ID: EMD-39676
TitleCryo-EM structure of cylindrical fiber of MyD88 TIR
Map data
Sample
  • Complex: signaling adopter protein in a self-assembled form
    • Protein or peptide: Myeloid differentiation primary response protein MyD88
Keywordssignaling protein / innate immunity / IMMUNE SYSTEM
Function / homology
Function and homology information


regulation of chemokine (C-X-C motif) ligand 1 production / MyD88 deficiency (TLR5) / TIR domain binding / ATP-dependent histone chaperone activity / Toll binding / toll-like receptor 5 signaling pathway / induced systemic resistance / regulation of chemokine (C-X-C motif) ligand 2 production / neutrophil-mediated killing of bacterium / leukocyte activation involved in inflammatory response ...regulation of chemokine (C-X-C motif) ligand 1 production / MyD88 deficiency (TLR5) / TIR domain binding / ATP-dependent histone chaperone activity / Toll binding / toll-like receptor 5 signaling pathway / induced systemic resistance / regulation of chemokine (C-X-C motif) ligand 2 production / neutrophil-mediated killing of bacterium / leukocyte activation involved in inflammatory response / response to molecule of fungal origin / positive regulation of lymphocyte proliferation / response to peptidoglycan / toll-like receptor 8 signaling pathway / positive regulation of interleukin-23 production / regulation of neutrophil migration / IRAK4 deficiency (TLR5) / establishment of endothelial intestinal barrier / MyD88 dependent cascade initiated on endosome / cellular response to oxidised low-density lipoprotein particle stimulus / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / Toll signaling pathway / Toll-like receptor binding / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / toll-like receptor TLR6:TLR2 signaling pathway / interleukin-33-mediated signaling pathway / neutrophil activation involved in immune response / microglia differentiation / RIP-mediated NFkB activation via ZBP1 / interleukin-1 receptor binding / death receptor binding / positive regulation of cytokine production involved in inflammatory response / MyD88 deficiency (TLR2/4) / extrinsic component of cytoplasmic side of plasma membrane / interleukin-1-mediated signaling pathway / extrinsic component of plasma membrane / IRAK4 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / positive regulation of macrophage cytokine production / 3'-UTR-mediated mRNA stabilization / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / type I interferon-mediated signaling pathway / skin development / defense response to protozoan / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of interleukin-17 production / response to amine / immunoglobulin mediated immune response / response to amino acid / positive regulation of type I interferon production / phagocytosis / positive regulation of chemokine production / JNK cascade / signaling adaptor activity / response to interleukin-1 / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / positive regulation of smooth muscle cell proliferation / positive regulation of JNK cascade / positive regulation of interleukin-6 production / Interleukin-1 signaling / cellular response to mechanical stimulus / positive regulation of NF-kappaB transcription factor activity / positive regulation of tumor necrosis factor production / PIP3 activates AKT signaling / ER-Phagosome pathway / cellular response to lipopolysaccharide / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / gene expression / molecular adaptor activity / defense response to virus / response to ethanol / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / endosome membrane / defense response to bacterium / innate immune response / apoptotic process / positive regulation of gene expression / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Myeloid differentiation primary response protein MyD88 / MyD88, death domain / TIR domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain ...Myeloid differentiation primary response protein MyD88 / MyD88, death domain / TIR domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Death-like domain superfamily
Similarity search - Domain/homology
Myeloid differentiation primary response protein MyD88
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKasai K / Imamura K / Narita A / Makino F / Miyata T / Kato T / Namba K / Onishi H / Tochio H
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR1762 Japan
Japan Society for the Promotion of Science (JSPS)16H04752 Japan
CitationJournal: Biorxiv / Year: 2024
Title: From Monomers to Oligomers: Structural Mechanism of Receptor-Triggered MyD88 Assembly in Innate Immune Signaling
Authors: Kasai K / Imamura K / Uno M / Sekiyama N / Miyata T / Makino F / Yamada R / Takahashi Y / Kodera N / Namba K / Ohnishi H / Narita A / Konno H / Tochio H
History
DepositionApr 4, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39676.png

Downloads & links

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Map

FileDownload / File: emd_39676.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 500 pix.
= 505. Å		1.01 Å/pix.
x 500 pix.
= 505. Å		1.01 Å/pix.
x 500 pix.
= 505. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.01 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.47019312 - 1.2569522
Average (Standard dev.)0.023673985 (±0.0802302)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 505.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39676_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_39676_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 : signaling adopter protein in a self-assembled form

EntireName: signaling adopter protein in a self-assembled form
Components
  • Complex: signaling adopter protein in a self-assembled form
    • Protein or peptide: Myeloid differentiation primary response protein MyD88

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Supramolecule #1: signaling adopter protein in a self-assembled form

SupramoleculeName: signaling adopter protein in a self-assembled form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.7 kDa/nm

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Macromolecule #1: Myeloid differentiation primary response protein MyD88

MacromoleculeName: Myeloid differentiation primary response protein MyD88
type: protein_or_peptide / ID: 1 / Number of copies: 104 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.841775 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
PLGHMPERFD AFICYCPSDI QFVQEMIRQL EQTNYRLKLC VSDRDVLPGT CVWSIASELI EKRCRRMVVV VSDDYLQSKE CDFQTKFAL SLSPGAHQKR LIPIKYKAMK KEFPSILRFI TVCDYTNPCT KSWFWTRLAK ALSLP

UniProtKB: Myeloid differentiation primary response protein MyD88

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

Concentration3.4 mg/mL
BufferpH: 7
Component:
ConcentrationNameFormula
20.0 mMHEPES-NaOH
50.0 mMsodium chlorideNaCl
10.0 mMdithiothreitolDTT
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 5325 / Average exposure time: 3.2 sec. / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ber

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26680
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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