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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) / 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)
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
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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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