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- PDB-8yym: Cryo-EM structure of cylindrical fiber of MyD88 TIR -

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Basic information

Entry
Database: PDB / ID: 8yym
TitleCryo-EM structure of cylindrical fiber of MyD88 TIR
ComponentsMyeloid differentiation primary response protein MyD88
KeywordsIMMUNE SYSTEM / signaling protein / innate immunity
Function / homology
Function and homology information


regulation of chemokine (C-X-C motif) ligand 1 production / MyD88 deficiency (TLR5) / Toll binding / toll-like receptor 5 signaling pathway / induced systemic resistance / ATP-dependent histone chaperone activity / TIR domain binding / 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) / Toll binding / toll-like receptor 5 signaling pathway / induced systemic resistance / ATP-dependent histone chaperone activity / TIR domain binding / 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 / toll-like receptor 8 signaling pathway / response to peptidoglycan / positive regulation of lymphocyte proliferation / positive regulation of interleukin-23 production / regulation of neutrophil migration / IRAK4 deficiency (TLR5) / establishment of endothelial intestinal barrier / MyD88 dependent cascade initiated on endosome / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / 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-like receptor binding / Toll signaling pathway / toll-like receptor TLR6:TLR2 signaling pathway / neutrophil activation involved in immune response / interleukin-33-mediated signaling pathway / microglia differentiation / RIP-mediated NFkB activation via ZBP1 / MyD88 deficiency (TLR2/4) / death receptor binding / interleukin-1 receptor binding / positive regulation of cytokine production involved in inflammatory response / interleukin-1-mediated signaling pathway / response to amine / IRAK4 deficiency (TLR2/4) / positive regulation of macrophage cytokine production / 3'-UTR-mediated mRNA stabilization / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extrinsic component of plasma membrane / toll-like receptor 4 signaling pathway / MyD88-dependent toll-like receptor signaling pathway / extrinsic component of cytoplasmic side of plasma membrane / skin development / type I interferon-mediated signaling pathway / defense response to protozoan / positive regulation of interleukin-17 production / immunoglobulin mediated immune response / positive regulation of NLRP3 inflammasome complex assembly / response to amino acid / phagocytosis / JNK cascade / positive regulation of chemokine production / positive regulation of type I interferon production / signaling adaptor activity / positive regulation of smooth muscle cell proliferation / lipopolysaccharide-mediated signaling pathway / p75NTR recruits signalling complexes / response to interleukin-1 / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / : / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / cellular response to mechanical stimulus / positive regulation of interleukin-6 production / positive regulation of JNK cascade / Interleukin-1 signaling / positive regulation of tumor necrosis factor production / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / ER-Phagosome pathway / cellular response to lipopolysaccharide / regulation of inflammatory response / gene expression / defense response to virus / molecular adaptor activity / response to ethanol / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / endosome membrane / defense response to bacterium / defense response to Gram-positive 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 / cytoplasm / cytosol
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)
MethodELECTRON MICROSCOPY / single 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, 2items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 6, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update
Revision 1.1May 6, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myeloid differentiation primary response protein MyD88
AA: Myeloid differentiation primary response protein MyD88
AB: Myeloid differentiation primary response protein MyD88
AC: Myeloid differentiation primary response protein MyD88
B: Myeloid differentiation primary response protein MyD88
BA: Myeloid differentiation primary response protein MyD88
BB: Myeloid differentiation primary response protein MyD88
BC: Myeloid differentiation primary response protein MyD88
C: Myeloid differentiation primary response protein MyD88
CA: Myeloid differentiation primary response protein MyD88
CB: Myeloid differentiation primary response protein MyD88
CC: Myeloid differentiation primary response protein MyD88
D: Myeloid differentiation primary response protein MyD88
DA: Myeloid differentiation primary response protein MyD88
DB: Myeloid differentiation primary response protein MyD88
DC: Myeloid differentiation primary response protein MyD88
E: Myeloid differentiation primary response protein MyD88
EA: Myeloid differentiation primary response protein MyD88
EB: Myeloid differentiation primary response protein MyD88
EC: Myeloid differentiation primary response protein MyD88
F: Myeloid differentiation primary response protein MyD88
FA: Myeloid differentiation primary response protein MyD88
FB: Myeloid differentiation primary response protein MyD88
FC: Myeloid differentiation primary response protein MyD88
G: Myeloid differentiation primary response protein MyD88
GA: Myeloid differentiation primary response protein MyD88
GB: Myeloid differentiation primary response protein MyD88
GC: Myeloid differentiation primary response protein MyD88
H: Myeloid differentiation primary response protein MyD88
HA: Myeloid differentiation primary response protein MyD88
HB: Myeloid differentiation primary response protein MyD88
HC: Myeloid differentiation primary response protein MyD88
I: Myeloid differentiation primary response protein MyD88
IA: Myeloid differentiation primary response protein MyD88
IB: Myeloid differentiation primary response protein MyD88
IC: Myeloid differentiation primary response protein MyD88
J: Myeloid differentiation primary response protein MyD88
JA: Myeloid differentiation primary response protein MyD88
JB: Myeloid differentiation primary response protein MyD88
JC: Myeloid differentiation primary response protein MyD88
K: Myeloid differentiation primary response protein MyD88
KA: Myeloid differentiation primary response protein MyD88
KB: Myeloid differentiation primary response protein MyD88
KC: Myeloid differentiation primary response protein MyD88
L: Myeloid differentiation primary response protein MyD88
LA: Myeloid differentiation primary response protein MyD88
LB: Myeloid differentiation primary response protein MyD88
LC: Myeloid differentiation primary response protein MyD88
M: Myeloid differentiation primary response protein MyD88
MA: Myeloid differentiation primary response protein MyD88
MB: Myeloid differentiation primary response protein MyD88
MC: Myeloid differentiation primary response protein MyD88
N: Myeloid differentiation primary response protein MyD88
NA: Myeloid differentiation primary response protein MyD88
NB: Myeloid differentiation primary response protein MyD88
NC: Myeloid differentiation primary response protein MyD88
O: Myeloid differentiation primary response protein MyD88
OA: Myeloid differentiation primary response protein MyD88
OB: Myeloid differentiation primary response protein MyD88
OC: Myeloid differentiation primary response protein MyD88
P: Myeloid differentiation primary response protein MyD88
PA: Myeloid differentiation primary response protein MyD88
PB: Myeloid differentiation primary response protein MyD88
PC: Myeloid differentiation primary response protein MyD88
Q: Myeloid differentiation primary response protein MyD88
QA: Myeloid differentiation primary response protein MyD88
QB: Myeloid differentiation primary response protein MyD88
QC: Myeloid differentiation primary response protein MyD88
R: Myeloid differentiation primary response protein MyD88
RA: Myeloid differentiation primary response protein MyD88
RB: Myeloid differentiation primary response protein MyD88
RC: Myeloid differentiation primary response protein MyD88
S: Myeloid differentiation primary response protein MyD88
SA: Myeloid differentiation primary response protein MyD88
SB: Myeloid differentiation primary response protein MyD88
SC: Myeloid differentiation primary response protein MyD88
T: Myeloid differentiation primary response protein MyD88
TA: Myeloid differentiation primary response protein MyD88
TB: Myeloid differentiation primary response protein MyD88
TC: Myeloid differentiation primary response protein MyD88
U: Myeloid differentiation primary response protein MyD88
UA: Myeloid differentiation primary response protein MyD88
UB: Myeloid differentiation primary response protein MyD88
UC: Myeloid differentiation primary response protein MyD88
V: Myeloid differentiation primary response protein MyD88
VA: Myeloid differentiation primary response protein MyD88
VB: Myeloid differentiation primary response protein MyD88
VC: Myeloid differentiation primary response protein MyD88
W: Myeloid differentiation primary response protein MyD88
WA: Myeloid differentiation primary response protein MyD88
WB: Myeloid differentiation primary response protein MyD88
WC: Myeloid differentiation primary response protein MyD88
X: Myeloid differentiation primary response protein MyD88
XA: Myeloid differentiation primary response protein MyD88
XB: Myeloid differentiation primary response protein MyD88
XC: Myeloid differentiation primary response protein MyD88
Y: Myeloid differentiation primary response protein MyD88
YA: Myeloid differentiation primary response protein MyD88
YB: Myeloid differentiation primary response protein MyD88
YC: Myeloid differentiation primary response protein MyD88
Z: Myeloid differentiation primary response protein MyD88
ZA: Myeloid differentiation primary response protein MyD88
ZB: Myeloid differentiation primary response protein MyD88
ZC: Myeloid differentiation primary response protein MyD88


Theoretical massNumber of molelcules
Total (without water)1,751,545104
Polymers1,751,545104
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Myeloid differentiation primary response protein MyD88


Mass: 16841.775 Da / Num. of mol.: 104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYD88 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99836
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: signaling adopter protein in a self-assembled form / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 5.7 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
120.0 mMHEPES-NaOH1
250.0 mMsodium chlorideNaCl1
310.0 mMdithiothreitolDTT1
SpecimenConc.: 3.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 3.2 sec. / Electron dose: 1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 5325

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Processing

EM softwareName: Gctf / Category: CTF correction
CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26680 / Symmetry type: POINT
RefinementStereochemistry target values: CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0058118352
ELECTRON MICROSCOPYf_angle_d0.6726159640
ELECTRON MICROSCOPYf_chiral_restr0.051317888
ELECTRON MICROSCOPYf_plane_restr0.007219760
ELECTRON MICROSCOPYf_dihedral_angle_d10.374573112

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