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- PDB-8w8m: Cryo-EM structure of helical filament of MyD88 TIR -

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Basic information

Entry
Database: PDB / ID: 8w8m
TitleCryo-EM structure of helical filament 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 / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / cellular response to oxidised low-density lipoprotein particle stimulus / 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 / positive regulation of cytokine production involved in inflammatory response / MyD88 deficiency (TLR2/4) / death receptor binding / interleukin-1-mediated signaling pathway / IRAK4 deficiency (TLR2/4) / positive regulation of macrophage cytokine production / extrinsic component of cytoplasmic side of plasma membrane / MyD88-dependent toll-like receptor signaling pathway / 3'-UTR-mediated mRNA stabilization / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extrinsic component of plasma membrane / toll-like receptor 4 signaling pathway / skin development / type I interferon-mediated signaling pathway / response to amine / defense response to protozoan / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of interleukin-17 production / immunoglobulin mediated immune response / positive regulation of type I interferon production / phagocytosis / response to amino acid / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of chemokine production / JNK cascade / signaling adaptor activity / positive regulation of smooth muscle cell proliferation / response to interleukin-1 / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / cellular response to mechanical stimulus / positive regulation of NF-kappaB transcription factor activity / Interleukin-1 signaling / positive regulation of interleukin-6 production / 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 / response to ethanol / molecular adaptor activity / defense response to virus / gene expression / cell surface receptor signaling pathway / endosome membrane / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-positive bacterium / 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: 3.28 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
DepositionSep 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D2: Myeloid differentiation primary response protein MyD88
D3: Myeloid differentiation primary response protein MyD88
E1: Myeloid differentiation primary response protein MyD88
E2: Myeloid differentiation primary response protein MyD88
E3: Myeloid differentiation primary response protein MyD88
F1: Myeloid differentiation primary response protein MyD88
F2: Myeloid differentiation primary response protein MyD88
F3: Myeloid differentiation primary response protein MyD88
D1: Myeloid differentiation primary response protein MyD88
A2: Myeloid differentiation primary response protein MyD88
A3: Myeloid differentiation primary response protein MyD88
B1: Myeloid differentiation primary response protein MyD88
B2: Myeloid differentiation primary response protein MyD88
B3: Myeloid differentiation primary response protein MyD88
C1: Myeloid differentiation primary response protein MyD88
C2: Myeloid differentiation primary response protein MyD88
C3: Myeloid differentiation primary response protein MyD88
A1: Myeloid differentiation primary response protein MyD88
J2: Myeloid differentiation primary response protein MyD88
J3: Myeloid differentiation primary response protein MyD88
K1: Myeloid differentiation primary response protein MyD88
K2: Myeloid differentiation primary response protein MyD88
K3: Myeloid differentiation primary response protein MyD88
L1: Myeloid differentiation primary response protein MyD88
L2: Myeloid differentiation primary response protein MyD88
L3: Myeloid differentiation primary response protein MyD88
J1: Myeloid differentiation primary response protein MyD88
G2: Myeloid differentiation primary response protein MyD88
G3: Myeloid differentiation primary response protein MyD88
H1: Myeloid differentiation primary response protein MyD88
H2: Myeloid differentiation primary response protein MyD88
H3: Myeloid differentiation primary response protein MyD88
I1: Myeloid differentiation primary response protein MyD88
I2: Myeloid differentiation primary response protein MyD88
I3: Myeloid differentiation primary response protein MyD88
G1: Myeloid differentiation primary response protein MyD88
M2: Myeloid differentiation primary response protein MyD88
M3: Myeloid differentiation primary response protein MyD88
N1: Myeloid differentiation primary response protein MyD88
N2: Myeloid differentiation primary response protein MyD88
N3: Myeloid differentiation primary response protein MyD88
O1: Myeloid differentiation primary response protein MyD88
O2: Myeloid differentiation primary response protein MyD88
O3: Myeloid differentiation primary response protein MyD88
M1: Myeloid differentiation primary response protein MyD88
P2: Myeloid differentiation primary response protein MyD88
P3: Myeloid differentiation primary response protein MyD88
Q1: Myeloid differentiation primary response protein MyD88
Q2: Myeloid differentiation primary response protein MyD88
Q3: Myeloid differentiation primary response protein MyD88
R1: Myeloid differentiation primary response protein MyD88
R2: Myeloid differentiation primary response protein MyD88
R3: Myeloid differentiation primary response protein MyD88
P1: Myeloid differentiation primary response protein MyD88
S2: Myeloid differentiation primary response protein MyD88
S3: Myeloid differentiation primary response protein MyD88
T1: Myeloid differentiation primary response protein MyD88
T2: Myeloid differentiation primary response protein MyD88
T3: Myeloid differentiation primary response protein MyD88
U1: Myeloid differentiation primary response protein MyD88
U2: Myeloid differentiation primary response protein MyD88
U3: Myeloid differentiation primary response protein MyD88
S1: Myeloid differentiation primary response protein MyD88
V2: Myeloid differentiation primary response protein MyD88
V3: Myeloid differentiation primary response protein MyD88
W1: Myeloid differentiation primary response protein MyD88
W2: Myeloid differentiation primary response protein MyD88
W3: Myeloid differentiation primary response protein MyD88
X1: Myeloid differentiation primary response protein MyD88
X2: Myeloid differentiation primary response protein MyD88
X3: Myeloid differentiation primary response protein MyD88
V1: Myeloid differentiation primary response protein MyD88
Y2: Myeloid differentiation primary response protein MyD88
Y3: Myeloid differentiation primary response protein MyD88
Z1: Myeloid differentiation primary response protein MyD88
Z2: Myeloid differentiation primary response protein MyD88
Z3: Myeloid differentiation primary response protein MyD88
1A: Myeloid differentiation primary response protein MyD88
2A: Myeloid differentiation primary response protein MyD88
3A: Myeloid differentiation primary response protein MyD88
Y1: Myeloid differentiation primary response protein MyD88
2B: Myeloid differentiation primary response protein MyD88
3B: Myeloid differentiation primary response protein MyD88
1C: Myeloid differentiation primary response protein MyD88
2C: Myeloid differentiation primary response protein MyD88
3C: Myeloid differentiation primary response protein MyD88
1D: Myeloid differentiation primary response protein MyD88
2D: Myeloid differentiation primary response protein MyD88
3D: Myeloid differentiation primary response protein MyD88
1B: Myeloid differentiation primary response protein MyD88
ZD: Myeloid differentiation primary response protein MyD88
YE: Myeloid differentiation primary response protein MyD88
ZE: Myeloid differentiation primary response protein MyD88
1E: Myeloid differentiation primary response protein MyD88
YF: Myeloid differentiation primary response protein MyD88
ZF: Myeloid differentiation primary response protein MyD88
1F: Myeloid differentiation primary response protein MyD88
YD: Myeloid differentiation primary response protein MyD88
2E: Myeloid differentiation primary response protein MyD88
3E: Myeloid differentiation primary response protein MyD88
2F: Myeloid differentiation primary response protein MyD88
3F: Myeloid differentiation primary response protein MyD88


Theoretical massNumber of molelcules
Total (without water)1,717,861102
Polymers1,717,861102
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.: 102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYD88 / Production host: Escherichia coli (E. coli) / 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: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 62.09 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0023116382
ELECTRON MICROSCOPYf_angle_d0.4419156876
ELECTRON MICROSCOPYf_chiral_restr0.042817544
ELECTRON MICROSCOPYf_plane_restr0.004519380
ELECTRON MICROSCOPYf_dihedral_angle_d3.766615096

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