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- EMDB-9064: Cryo-EM structure of the PYD filament of AIM2 -

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Basic information

Entry
Database: EMDB / ID: EMD-9064
TitleCryo-EM structure of the PYD filament of AIM2
Map dataPYD filament of AIM2
Sample
  • Organelle or cellular component: PYD of AIM2
    • Protein or peptide: Interferon-inducible protein AIM2
    • Protein or peptide: Green fluorescent protein
KeywordsFilament / higher order / innate immunity / inflammasome / IMMUNE SYSTEM
Function / homology
Function and homology information


pyroptosome complex assembly / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / regulation of behavior / cysteine-type endopeptidase activator activity / Cytosolic sensors of pathogen-associated DNA / pattern recognition receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / pattern recognition receptor activity ...pyroptosome complex assembly / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / regulation of behavior / cysteine-type endopeptidase activator activity / Cytosolic sensors of pathogen-associated DNA / pattern recognition receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / pattern recognition receptor activity / pyroptotic inflammatory response / T cell homeostasis / cellular response to interferon-beta / positive regulation of defense response to virus by host / signaling adaptor activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / activation of innate immune response / bioluminescence / positive regulation of interleukin-1 beta production / tumor necrosis factor-mediated signaling pathway / generation of precursor metabolites and energy / positive regulation of NF-kappaB transcription factor activity / brain development / neuron cellular homeostasis / cellular response to xenobiotic stimulus / positive regulation of inflammatory response / site of double-strand break / double-stranded DNA binding / defense response to virus / immune response / innate immune response / DNA damage response / mitochondrion / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
HIN-200/IF120x / HIN-200/IF120x domain / HIN-200 A and B domains profile. / HIN-200 family / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Green fluorescent protein, GFP / Death-like domain superfamily ...HIN-200/IF120x / HIN-200/IF120x domain / HIN-200 A and B domains profile. / HIN-200 family / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Green fluorescent protein, GFP / Death-like domain superfamily / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Interferon-inducible protein AIM2 / Green fluorescent protein
Similarity search - Component
Biological speciesHomo sapiens (human) / Aequorea victoria (jellyfish)
Methodhelical reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsLu A / Li Y
CitationJournal: Cell Discov / Year: 2015
Title: Plasticity in PYD assembly revealed by cryo-EM structure of the PYD filament of AIM2.
Authors: Alvin Lu / Yang Li / Qian Yin / Jianbin Ruan / Xiong Yu / Edward Egelman / Hao Wu /
Abstract: Absent in melanoma 2 (AIM2) is an essential cytosolic double-stranded DNA receptor that assembles with the adaptor, apoptosis-associated speck-like protein containing a caspase recruitment domain ...Absent in melanoma 2 (AIM2) is an essential cytosolic double-stranded DNA receptor that assembles with the adaptor, apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC), and caspase-1 to form the AIM2 inflammasome, which leads to proteolytic maturation of cytokines and pyroptotic cell death. AIM2 contains an N-terminal Pyrin domain (PYD) that interacts with ASC through PYD/PYD interactions and nucleates ASC filament formation. To elucidate the molecular basis of AIM2-induced ASC polymerization, we generated AIM2 filaments fused to green fluorescent protein (GFP) and determined its cryo-electron microscopic (cryo-EM) structure. The map showed distinct definition of helices, allowing fitting of the crystal structure. Surprisingly, the GFP-AIM2 filament is a 1-start helix with helical parameters distinct from those of the 3-start ASC filament. However, despite the apparent symmetry difference, helical net and detailed interface analyses reveal minimal changes in subunit packing. GFP-AIM2 nucleated ASC filament formation in comparable efficiency as untagged AIM2, suggesting assembly plasticity in both AIM2 and ASC. The DNA-binding domain of AIM2 is able to form AIM2/DNA filaments, within which the AIM2 is brought into proximity to template ASC filament assembly. Because ASC is able to interact with many PYD-containing receptors for the formation of inflammasomes, the observed structural plasticity may be critically important for this versatility in the PYD/PYD interactions.
History
DepositionAug 29, 2018-
Header (metadata) releaseSep 5, 2018-
Map releaseSep 5, 2018-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1000
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1000
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6mb2
  • Surface level: 1000
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9064.png

Downloads & links

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Map

FileDownload / File: emd_9064.map.gz / Format: CCP4 / Size: 112.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPYD filament of AIM2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.58 Å/pix.
x 200 pix.
= 115. Å		0.58 Å/pix.
x 384 pix.
= 220.8 Å		0.58 Å/pix.
x 384 pix.
= 220.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.575 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1000.0 / Movie #1: 1000
Minimum - Maximum51.663567 - 1369.084499999999935
Average (Standard dev.)521.985400000000027 (±287.610380000000021)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-99
Dimensions384384200
Spacing384384200
CellA: 220.79999 Å / B: 220.79999 Å / C: 115.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.5750.5750.575
M x/y/z384384200
origin x/y/z0.0000.0000.000
length x/y/z220.800220.800115.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-192-192-99
NC/NR/NS384384200
D min/max/mean51.6641369.084521.985

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Supplemental data

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Sample components

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Entire : PYD of AIM2

EntireName: PYD of AIM2
Components
  • Organelle or cellular component: PYD of AIM2
    • Protein or peptide: Interferon-inducible protein AIM2
    • Protein or peptide: Green fluorescent protein

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Supramolecule #1: PYD of AIM2

SupramoleculeName: PYD of AIM2 / type: organelle_or_cellular_component / 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: 15 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.839629 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AMESKYKEIL LLTGLDNITD EELDRFKGFL SDEFNIATGK LHTANRIQVA TLMIQNAGAV SAVMKTIRIF QKLNYMLLAK RLQEEKEKV DKQYK

UniProtKB: Interferon-inducible protein AIM2

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Macromolecule #2: Green fluorescent protein

MacromoleculeName: Green fluorescent protein / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 25.924553 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SKGEELFTGV VPILVELDGD VNGHKFSVSG EGEGDATYGK LTLKFICTTG KLPVPWPTLV TTF(CRO)VQCFSR YPDH (MSE)KRHD FFKSA(MSE)PEGY VQERTIFFKD DGNYKTRAEV KFEGDTLVNR IELKGIDFKE DGNILGHKLE YNYNSHN VY I(MSE)ADKQKNGI ...String:
SKGEELFTGV VPILVELDGD VNGHKFSVSG EGEGDATYGK LTLKFICTTG KLPVPWPTLV TTF(CRO)VQCFSR YPDH (MSE)KRHD FFKSA(MSE)PEGY VQERTIFFKD DGNYKTRAEV KFEGDTLVNR IELKGIDFKE DGNILGHKLE YNYNSHN VY I(MSE)ADKQKNGI KVNFKIRHNI EDGSVQLADH YQQNTPIGDG PVLLPDNHYL STQSALSKDP NEKRDH(MSE)VLL EFVTAAGI

UniProtKB: Green fluorescent protein

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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
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 6.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 138.9 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 54973
Startup modelType of model: OTHER / Details: Solid cylinder
Final angle assignmentType: NOT APPLICABLE

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