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- EMDB-22656: Cryo-EM structure of AIM2-PYD filament -

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Basic information

Entry
Database: EMDB / ID: EMD-22656
TitleCryo-EM structure of AIM2-PYD filament
Map dataCryo-EM structure of AIM2-PYD filament
Sample
  • Complex: AIM2-PYD filament
    • Protein or peptide: Interferon-inducible protein AIM2
KeywordsInflammasome / AIM2 filament / Helical reconstruction / PROTEIN FIBRIL
Function / homology
Function and homology information


pyroptosome complex assembly / AIM2 inflammasome complex assembly / The AIM2 inflammasome / cysteine-type endopeptidase activator activity / regulation of behavior / AIM2 inflammasome complex / Cytosolic sensors of pathogen-associated DNA / positive regulation of cysteine-type endopeptidase activity / pattern recognition receptor signaling pathway / pattern recognition receptor activity ...pyroptosome complex assembly / AIM2 inflammasome complex assembly / The AIM2 inflammasome / cysteine-type endopeptidase activator activity / regulation of behavior / AIM2 inflammasome complex / Cytosolic sensors of pathogen-associated DNA / positive regulation of cysteine-type endopeptidase activity / pattern recognition receptor signaling pathway / pattern recognition receptor activity / negative regulation of NF-kappaB transcription factor activity / pyroptotic inflammatory response / T cell homeostasis / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to interferon-beta / signaling adaptor activity / positive regulation of defense response to virus by host / tumor necrosis factor-mediated signaling pathway / activation of innate immune response / positive regulation of interleukin-1 beta production / brain development / neuron cellular homeostasis / positive regulation of inflammatory response / cellular response to xenobiotic stimulus / positive regulation of NF-kappaB transcription factor activity / site of double-strand break / double-stranded DNA binding / defense response to virus / inflammatory response / immune response / innate immune response / DNA damage response / mitochondrion / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
HIN-200/IF120x / HIN-200 family / HIN-200/IF120x domain / HIN-200 A and B domains profile. / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Death-like domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Interferon-inducible protein AIM2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZheng W / Matyszewski M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
CitationJournal: Nat Commun / Year: 2021
Title: Distinct axial and lateral interactions within homologous filaments dictate the signaling specificity and order of the AIM2-ASC inflammasome.
Authors: Mariusz Matyszewski / Weili Zheng / Jacob Lueck / Zachary Mazanek / Naveen Mohideen / Albert Y Lau / Edward H Egelman / Jungsan Sohn /
Abstract: Inflammasomes are filamentous signaling platforms integral to innate immunity. Currently, little is known about how these structurally similar filaments recognize and distinguish one another. A cryo- ...Inflammasomes are filamentous signaling platforms integral to innate immunity. Currently, little is known about how these structurally similar filaments recognize and distinguish one another. A cryo-EM structure of the AIM2 filament reveals that the architecture of the upstream filament is essentially identical to that of the adaptor ASC filament. In silico simulations using Rosetta and molecular dynamics followed by biochemical and cellular experiments consistently demonstrate that individual filaments assemble bidirectionally. By contrast, the recognition between AIM2 and ASC requires at least one to be oligomeric and occurs in a head-to-tail manner. Using in silico mutagenesis as a guide, we also identify specific axial and lateral interfaces that dictate the recognition and distinction between AIM2 and ASC filaments. Together, the results here provide a robust framework for delineating the signaling specificity and order of inflammasomes.
History
DepositionSep 12, 2020-
Header (metadata) releaseMay 26, 2021-
Map releaseMay 26, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.000109
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.000109
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7k3r
  • Surface level: 0.000109
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7k3r
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22656.png

Downloads & links

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Map

FileDownload / File: emd_22656.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of AIM2-PYD filament
Voxel sizeX=Y=Z: 0.66 Å
Density
Contour LevelBy AUTHOR: 0.000109 / Movie #1: 0.000109
Minimum - Maximum-0.00016584854 - 0.0003695768
Average (Standard dev.)0.000003939982 (±0.000035127396)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 168.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.660.660.66
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z168.960168.960168.960
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-0.0000.0000.000

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Supplemental data

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Sample components

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Entire : AIM2-PYD filament

EntireName: AIM2-PYD filament
Components
  • Complex: AIM2-PYD filament
    • Protein or peptide: Interferon-inducible protein AIM2

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Supramolecule #1: AIM2-PYD filament

SupramoleculeName: AIM2-PYD filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Interferon-inducible protein AIM2

MacromoleculeName: Interferon-inducible protein AIM2 / type: protein_or_peptide / ID: 1 / Number of copies: 21 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.528655 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GTGMESKYKE ILLLTGLDNI TDEELDRFKF FLSDEFNIAT GKLHTANRIQ VATLMIQNAG AVSAVMKTIR IFQKLNYMLL AKRLQEEKE KVDKQYKSVT KPKPLSQAEM SPAASAAIRN D

UniProtKB: Interferon-inducible protein AIM2

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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: 7.5
GridPretreatment - Type: PLASMA CLEANING / Details: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 14.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 53.3 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPIDER / Number images used: 99237
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4o7q

Final angle assignmentType: NOT APPLICABLE

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