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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
Function / homology
Function and homology information


regulation of chemokine (C-X-C motif) ligand 1 production / Toll binding / MyD88 deficiency (TLR5) / regulation of chemokine (C-X-C motif) ligand 2 production / ATP-dependent histone chaperone activity / neutrophil-mediated killing of bacterium / induced systemic resistance / leukocyte activation involved in inflammatory response / TIR domain binding / response to molecule of fungal origin ...regulation of chemokine (C-X-C motif) ligand 1 production / Toll binding / MyD88 deficiency (TLR5) / regulation of chemokine (C-X-C motif) ligand 2 production / ATP-dependent histone chaperone activity / neutrophil-mediated killing of bacterium / induced systemic resistance / leukocyte activation involved in inflammatory response / TIR domain binding / 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 / establishment of endothelial intestinal barrier / IRAK4 deficiency (TLR5) / regulation of neutrophil migration / 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 / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / neutrophil activation involved in immune response / interleukin-33-mediated signaling pathway / Toll-like receptor binding / microglia differentiation / RIP-mediated NFkB activation via ZBP1 / positive regulation of cytokine production involved in inflammatory response / interleukin-1 receptor binding / death receptor binding / MyD88 deficiency (TLR2/4) / positive regulation of macrophage cytokine production / MyD88-dependent toll-like receptor signaling pathway / interleukin-1-mediated signaling pathway / IRAK4 deficiency (TLR2/4) / skin development / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / 3'-UTR-mediated mRNA stabilization / positive regulation of NLRP3 inflammasome complex assembly / extrinsic component of plasma membrane / immune system process / type I interferon-mediated signaling pathway / defense response to protozoan / positive regulation of interleukin-17 production / response to amine / immunoglobulin mediated immune response / positive regulation of type I interferon production / response to amino acid / signaling adaptor activity / phagocytosis / positive regulation of chemokine production / JNK cascade / lipopolysaccharide-mediated signaling pathway / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / extrinsic component of cytoplasmic side of plasma membrane / response to interleukin-1 / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / positive regulation of smooth muscle cell proliferation / response to organic cyclic compound / positive regulation of interleukin-6 production / Interleukin-1 signaling / cellular response to mechanical stimulus / : / positive regulation of tumor necrosis factor production / PIP3 activates AKT signaling / gene expression / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / response to ethanol / cellular response to lipopolysaccharide / cell surface receptor signaling pathway / molecular adaptor activity / endosome membrane / 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 / Penczek PAP / Gay NJ
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-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.09
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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)
Voxel sizeX=Y=Z: 1.06 Å
Density
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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_4405_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_4405_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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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)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

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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 chloridesodium 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
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 FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.1 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 0.92 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.0/3.0) / Software - details: Relion was used for refinement
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
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3mop


Chain - Chain ID: A
RefinementProtocol: OTHER
Output model

PDB-6i3n:
Helical MyD88 death domain filament

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