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- PDB-6i3n: Helical MyD88 death domain filament -

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Basic information

Entry
Database: PDB / ID: 6i3n
TitleHelical MyD88 death domain filament
ComponentsMyeloid differentiation primary response protein MyD88
KeywordsSIGNALING PROTEIN / helix / filament / TLR
Function / homology
Function and homology information


MyD88 deficiency (TLR5) / Toll binding / toll-like receptor 5 signaling pathway / ATP-dependent histone chaperone activity / TIR domain binding / toll-like receptor 8 signaling pathway / positive regulation of interleukin-23 production / IRAK4 deficiency (TLR5) / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / MyD88 dependent cascade initiated on endosome ...MyD88 deficiency (TLR5) / Toll binding / toll-like receptor 5 signaling pathway / ATP-dependent histone chaperone activity / TIR domain binding / toll-like receptor 8 signaling pathway / positive regulation of interleukin-23 production / IRAK4 deficiency (TLR5) / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / 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 / Toll-like receptor binding / MyD88 cascade initiated on plasma membrane / toll-like receptor TLR6:TLR2 signaling pathway / Toll signaling pathway / interleukin-33-mediated signaling pathway / regulation of MAP kinase activity / NLRP3 inflammasome complex assembly / RIP-mediated NFkB activation via ZBP1 / death receptor binding / MyD88 deficiency (TLR2/4) / interleukin-1 receptor binding / response to amine / interleukin-1-mediated signaling pathway / toll-like receptor 4 signaling pathway / 3'-UTR-mediated mRNA stabilization / positive regulation of cytokine production involved in inflammatory response / IRAK4 deficiency (TLR2/4) / skin development / extrinsic component of plasma membrane / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / MyD88-dependent toll-like receptor signaling pathway / defense response to protozoan / extrinsic component of cytoplasmic side of plasma membrane / toll-like receptor signaling pathway / type I interferon-mediated signaling pathway / positive regulation of interleukin-17 production / positive regulation of NLRP3 inflammasome complex assembly / response to amino acid / JNK cascade / phagocytosis / canonical NF-kappaB signal transduction / immune system process / positive regulation of type I interferon production / positive regulation of smooth muscle cell proliferation / signaling adaptor activity / response to interleukin-1 / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of interleukin-8 production / positive regulation of interleukin-1 beta production / cellular response to mechanical stimulus / positive regulation of interleukin-6 production / gene expression / Interleukin-1 signaling / PIP3 activates AKT signaling / regulation of inflammatory response / cellular response to lipopolysaccharide / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / ER-Phagosome pathway / defense response to virus / molecular adaptor activity / response to ethanol / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / defense response to bacterium / endosome membrane / defense response to Gram-positive bacterium / inflammatory response / innate immune response / positive regulation of gene expression / apoptotic process / 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 / Death Domain, Fas / Death Domain, Fas / TIR domain / TIR domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain ...Myeloid differentiation primary response protein MyD88 / MyD88, death domain / Death Domain, Fas / Death Domain, Fas / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Myeloid differentiation primary response protein MyD88 / Myeloid differentiation primary response protein MyD88
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMoncrieffe, M.C. / Bollschweiler, D. / Penczek, P.A.P. / Gay, N.J.
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, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.2Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
M: Myeloid differentiation primary response protein MyD88
I: Myeloid differentiation primary response protein MyD88
J: Myeloid differentiation primary response protein MyD88
K: Myeloid differentiation primary response protein MyD88
H: Myeloid differentiation primary response protein MyD88
L: Myeloid differentiation primary response protein MyD88
B: Myeloid differentiation primary response protein MyD88
F: Myeloid differentiation primary response protein MyD88
C: Myeloid differentiation primary response protein MyD88
D: Myeloid differentiation primary response protein MyD88
A: Myeloid differentiation primary response protein MyD88
E: Myeloid differentiation primary response protein MyD88
G: Myeloid differentiation primary response protein MyD88


Theoretical massNumber of molelcules
Total (without water)229,40913
Polymers229,40913
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area27660 Å2
ΔGint-68 kcal/mol
Surface area53960 Å2
MethodPISA

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Components

#1: Protein
Myeloid differentiation primary response protein MyD88


Mass: 17646.873 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYD88 / Production host: Escherichia coli (E. coli) / References: UniProt: H0Y4G9, UniProt: Q99836*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Human MyD88 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
130 mMsodium chlorideNaCl1
220 mMTris1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 3100 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 900 nm / Calibrated defocus max: 3200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 0.92 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14rc2_3191: / Classification: refinement
EM software
IDNameVersionCategoryDetails (eV)
1RELION3particle selection
4Gctf1.06CTF correction
7MOLREP11.6model fitting
9SPHIRE1initial Euler assignmentSPHIRE was used for indexing
10RELION2.0/3.0final Euler assignmentRelion was used for refinement
12RELION33D reconstruction
13PHENIX1.14model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 98.01 ° / Axial rise/subunit: 5.98 Å / Axial symmetry: C1
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1229488 / Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER
Atomic model buildingPDB-ID: 3MOP

3mop


Pdb chain-ID: A / Accession code: 3MOP / Source name: PDB / Type: experimental model

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