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- EMDB-8625: Cryo-EM structure of the MAL TIR domain filament -

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Basic information

Entry
Database: EMDB / ID: 8625
TitleCryo-EM structure of the MAL TIR domain filament
Map dataCryo-EM structure of the MAL TIR domain filament
SampleMAL TIR domain filament
  • Toll/interleukin-1 receptor domain-containing adapter protein
Function / homologyTIR domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / IRAK4 deficiency (TLR2/4) / MyD88 deficiency (TLR2/4) / MyD88:Mal cascade initiated on plasma membrane / Toll-interleukin 1 receptor domain-containing adaptor protein, Tirap / Toll/interleukin-1 receptor homology (TIR) domain / TIR domain profile. / ER-Phagosome pathway / TIRAP-dependent toll-like receptor 4 signaling pathway ...TIR domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / IRAK4 deficiency (TLR2/4) / MyD88 deficiency (TLR2/4) / MyD88:Mal cascade initiated on plasma membrane / Toll-interleukin 1 receptor domain-containing adaptor protein, Tirap / Toll/interleukin-1 receptor homology (TIR) domain / TIR domain profile. / ER-Phagosome pathway / TIRAP-dependent toll-like receptor 4 signaling pathway / positive regulation of interleukin-15 production / positive regulation of chemokine (C-X-C motif) ligand 1 production / regulation of interferon-beta production / cellular response to bacterial lipopeptide / Toll-like receptor 4 binding / positive regulation of toll-like receptor 3 signaling pathway / positive regulation of toll-like receptor 2 signaling pathway / Toll-like receptor 2 binding / positive regulation of interleukin-6 biosynthetic process / myeloid cell differentiation / positive regulation of protein homodimerization activity / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of neutrophil chemotaxis / negative regulation of growth of symbiont in host / positive regulation of toll-like receptor 4 signaling pathway / regulation of innate immune response / activation of NF-kappaB-inducing kinase activity / positive regulation of interleukin-12 production / 3'-UTR-mediated mRNA stabilization / positive regulation of interleukin-8 production / cellular response to lipoteichoic acid / positive regulation of B cell proliferation / protein kinase C binding / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of tumor necrosis factor production / positive regulation of JNK cascade / endocytic vesicle / MyD88-dependent toll-like receptor signaling pathway / protein binding, bridging / ruffle membrane / positive regulation of I-kappaB kinase/NF-kappaB signaling / response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / defense response to Gram-positive bacterium / inflammatory response / innate immune response / protein heterodimerization activity / protein homodimerization activity / identical protein binding / plasma membrane / cytosol / cytoplasm / Toll/interleukin-1 receptor domain-containing adapter protein
Function and homology information
SourceHomo sapiens (human)
Methodhelical reconstruction / cryo EM / 7 Å resolution
AuthorsVe T / Vajjhala PR
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Structural basis of TIR-domain-assembly formation in MAL- and MyD88-dependent TLR4 signaling.
Authors: Thomas Ve / Parimala R Vajjhala / Andrew Hedger / Tristan Croll / Frank DiMaio / Shane Horsefield / Xiong Yu / Peter Lavrencic / Zahid Hassan / Garry P Morgan / Ashley Mansell / Mehdi Mobli / Ailis O'Carroll / Brieuc Chauvin / Yann Gambin / Emma Sierecki / Michael J Landsberg / Katryn J Stacey / Edward H Egelman / Bostjan Kobe
Validation ReportPDB-ID: 5uzb

SummaryFull reportAbout validation report
DateDeposition: Feb 25, 2017 / Header (metadata) release: Jul 26, 2017 / Map release: Jul 26, 2017 / Last update: Sep 20, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 350
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 350
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5uzb
  • Surface level: 350
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5uzb
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8625.map.gz (map file in CCP4 format, 27041 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
1.07 Å/pix.
= 107. Å
260 pix
1.07 Å/pix.
= 278.2 Å
260 pix
1.07 Å/pix.
= 278.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour Level:350 (by author), 350 (movie #1):
Minimum - Maximum-211.08592 - 781.7997
Average (Standard dev.)102.514694 (152.01855)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions260260100
Origin-130-130-49
Limit12912950
Spacing260260100
CellA: 278.2 Å / B: 278.2 Å / C: 107.00001 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z260260100
origin x/y/z0.0000.0000.000
length x/y/z278.200278.200107.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-130-130-49
NC/NR/NS260260100
D min/max/mean-211.086781.800102.515

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Supplemental data

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Sample components

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Entire MAL TIR domain filament

EntireName: MAL TIR domain filament / Number of components: 2

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Component #1: protein, MAL TIR domain filament

ProteinName: MAL TIR domain filament / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Toll/interleukin-1 receptor domain-containing adapter protein

ProteinName: Toll/interleukin-1 receptor domain-containing adapter protein
Recombinant expression: No
MassTheoretical: 19.689162 kDa
Source (engineered)Expression System: Homo sapiens (human) / Vector: pMCSG7

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Experimental details

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Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C6 (6 fold cyclic) / Delta z: 15.5 Å / Delta phi: -26.8 deg.
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 446

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: SPIDER, IHRSR / Resolution: 7 Å / Resolution method: OTHER

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Atomic model buiding

Output model

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