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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


MyD88 deficiency (TLR5) / Toll binding / toll-like receptor 5 signaling pathway / ATP-dependent histone chaperone activity / TIR domain binding / toll-like receptor 8 signaling pathway / positive regulation of interleukin-23 production / IRAK4 deficiency (TLR5) / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / MyD88 dependent cascade initiated on endosome ...MyD88 deficiency (TLR5) / Toll binding / toll-like receptor 5 signaling pathway / ATP-dependent histone chaperone activity / TIR domain binding / toll-like receptor 8 signaling pathway / positive regulation of interleukin-23 production / IRAK4 deficiency (TLR5) / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / 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 / Toll-like receptor binding / MyD88 cascade initiated on plasma membrane / toll-like receptor TLR6:TLR2 signaling pathway / Toll signaling pathway / interleukin-33-mediated signaling pathway / regulation of MAP kinase activity / NLRP3 inflammasome complex assembly / RIP-mediated NFkB activation via ZBP1 / death receptor binding / MyD88 deficiency (TLR2/4) / interleukin-1 receptor binding / interleukin-1-mediated signaling pathway / response to amine / toll-like receptor 4 signaling pathway / positive regulation of cytokine production involved in inflammatory response / 3'-UTR-mediated mRNA stabilization / skin development / IRAK4 deficiency (TLR2/4) / extrinsic component of plasma membrane / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / MyD88-dependent toll-like receptor signaling pathway / defense response to protozoan / extrinsic component of cytoplasmic side of plasma membrane / toll-like receptor signaling pathway / type I interferon-mediated signaling pathway / positive regulation of interleukin-17 production / positive regulation of NLRP3 inflammasome complex assembly / response to amino acid / JNK cascade / phagocytosis / canonical NF-kappaB signal transduction / positive regulation of type I interferon production / positive regulation of smooth muscle cell proliferation / signaling adaptor activity / response to interleukin-1 / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of interleukin-8 production / positive regulation of interleukin-1 beta production / cellular response to mechanical stimulus / positive regulation of interleukin-6 production / gene expression / Interleukin-1 signaling / PIP3 activates AKT signaling / cellular response to lipopolysaccharide / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / ER-Phagosome pathway / regulation of inflammatory response / defense response to virus / molecular adaptor activity / response to ethanol / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / defense response to bacterium / endosome membrane / defense response to Gram-positive bacterium / innate immune response / positive regulation of gene expression / apoptotic process / 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
Citation
Journal: Nat Commun / Year: 2026
Title: Structural Mechanism of Receptor-Triggered MyD88 Oligomeric Assembly in Innate Immune Signaling.
Authors: Kazuki Kasai / Kayo Imamura / Masatoshi Uno / Shiho Nukui / Naotaka Sekiyama / Tomoko Miyata / Fumiaki Makino / Ryusei Yamada / Yoshiki Takahashi / Noriyuki Kodera / Keiichi Namba / Hidenori ...Authors: Kazuki Kasai / Kayo Imamura / Masatoshi Uno / Shiho Nukui / Naotaka Sekiyama / Tomoko Miyata / Fumiaki Makino / Ryusei Yamada / Yoshiki Takahashi / Noriyuki Kodera / Keiichi Namba / Hidenori Ohnishi / Akihiro Narita / Hiroki Konno / Hidehito Tochio /
Abstract: MyD88 plays a pivotal role in Toll-like receptor (TLR) and interleukin-1 family signaling through its oligomerization upon receptor activation, leading to downstream protein recruitment. The ...MyD88 plays a pivotal role in Toll-like receptor (TLR) and interleukin-1 family signaling through its oligomerization upon receptor activation, leading to downstream protein recruitment. The Toll/interleukin-1 receptor domain of MyD88 (TIR) is responsible for this receptor-mediated oligomerization, but the detailed mechanism involved remains elusive. Here we investigate the structure of TIR oligomers and their interactions with TLRs. Cryoelectron microscopy reveals that tandemly arrayed TIR subunits form an antiparallel double-stranded filament that can further form rings and cylindrical filaments. Moreover, the self-assembly of TIR in vitro is markedly accelerated by dimeric rather than monomeric receptor TIRs, possibly reflecting the signal initiation step in vivo. High-speed atomic force microscopy further captures the dynamic processes of oligomerization of TIR, in addition to its direct interaction with the receptor TIRs. These results reveal a regulatory mechanism of TIR oligomerization underlying the signal initiation step.
#1: Journal: 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-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing 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
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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

CTF correctionSoftware - Name: Gctf / Type: NONE
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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