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- EMDB-4405: Helical MyD88 death domain filament -

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Basic information

Entry
Database: EMDB / ID: EMD-4405
TitleHelical MyD88 death domain filament
Map data
Sample
  • Complex: Human MyD88
    • Protein or peptide: Myeloid differentiation primary response protein MyD88
Keywordshelix / filament / TLR / SIGNALING PROTEIN
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 / immune system process / 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 / inflammatory response / 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 / 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. ...Myeloid differentiation primary response protein MyD88 / MyD88, death domain / TIR 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 / Myeloid differentiation primary response protein MyD88
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMoncrieffe MC / Bollschweiler D
CitationJournal: Structure / Year: 2020
Title: MyD88 Death-Domain Oligomerization Determines Myddosome Architecture: Implications for Toll-like Receptor Signaling.
Authors: Martin C Moncrieffe / Daniel Bollschweiler / Bing Li / Pawel A Penczek / Lee Hopkins / Clare E Bryant / David Klenerman / Nicholas J Gay /
Abstract: Toll-like receptors (TLRs) are pivotal in triggering the innate immune response to pathogen infection. Ligand binding induces receptor dimerization which facilitates the recruitment of other post- ...Toll-like receptors (TLRs) are pivotal in triggering the innate immune response to pathogen infection. Ligand binding induces receptor dimerization which facilitates the recruitment of other post-receptor signal transducers into a complex signalosome, the Myddosome. Central to this process is Myeloid differentiation primary response 88 (MyD88), which is required by almost all TLRs, and signaling is thought to proceed via the stepwise, sequential assembly of individual components. Here, we show that the death domains of human MyD88 spontaneously and reversibly associate to form helical filaments in vitro. A 3.1-Å cryoelectron microscopy structure reveals that the architecture of the filament is identical to that of the 6:4 MyD88-IRAK4-IRAK2 hetero-oligomeric Myddosome. Additionally, the death domain of IRAK4 interacts with the filaments to reconstitute the non-stoichiometric 6:4 MyD88-IRAK4 complex. Together, these data suggest that intracellularly, the MyD88 scaffold may be pre-formed and poised for recruitment of IRAKs on receptor activation and TIR engagement.
History
DepositionNov 6, 2018-
Header (metadata) releaseNov 20, 2019-
Map releaseNov 20, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
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  • Surface view colored by cylindrical radius
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  • Surface view with fitted model
  • Atomic models: PDB-6i3n
  • Surface level: 0.09
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6i3n
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4405.png

Downloads & links

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Map

FileDownload / File: emd_4405.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 220 pix.
= 233.2 Å		1.06 Å/pix.
x 220 pix.
= 233.2 Å		1.06 Å/pix.
x 220 pix.
= 233.2 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.31273994 - 0.58012915
Average (Standard dev.)0.002414341 (±0.024848556)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 233.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z233.200233.200233.200
α/β/γ90.00090.00090.000
start NX/NY/NZ929262
NX/NY/NZ290290360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.3130.5800.002

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Supplemental data

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Mask #1

Fileemd_4405_msk_1.map
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Half map: #1

Fileemd_4405_half_map_1.map
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Half map: #2

Fileemd_4405_half_map_2.map
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Sample components

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Entire : Human MyD88

EntireName: Human MyD88
Components
  • Complex: Human MyD88
    • Protein or peptide: Myeloid differentiation primary response protein MyD88

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Supramolecule #1: Human MyD88

SupramoleculeName: Human MyD88 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: 13 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.646873 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SNAMAAGGPG AGSAAPVSST SSLPLAALNM RVRRRLSLFL NVRTQVAADW TALAEEMDFE YLEIRQLETQ ADPTGRLLDA WQGRPGASV GRLLELLTKL GRDDVLLELG PSIEEDCQKY ILKQQQEEAE KPLQVAAVDS SVPRTAELAG ITTLDWSHPQ F EK

UniProtKB: Myeloid differentiation primary response protein MyD88

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
30.0 mMNaClsodium chloride
20.0 mMTris
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 0.92 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.2 µm / Calibrated defocus min: 0.9 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.1 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.98 Å
Applied symmetry - Helical parameters - Δ&Phi: 98.01 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 1229488
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.0/3.0) / Software - details: Relion was used for refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3mop


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: OTHER
Output model

PDB-6i3n:
Helical MyD88 death domain filament

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