+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9064 | |||||||||
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Title | Cryo-EM structure of the PYD filament of AIM2 | |||||||||
Map data | PYD filament of AIM2 | |||||||||
Sample |
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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 / positive regulation of cysteine-type endopeptidase activity / pattern recognition receptor activity / pattern recognition receptor signaling pathway ...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 / positive regulation of cysteine-type endopeptidase activity / pattern recognition receptor activity / pattern recognition receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / pyroptosis / 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 / bioluminescence / generation of precursor metabolites and energy / positive regulation of interleukin-1 beta production / brain development / positive regulation of inflammatory response / neuron cellular homeostasis / cellular response to xenobiotic stimulus / site of double-strand break / positive regulation of NF-kappaB transcription factor activity / double-stranded DNA binding / defense response to virus / immune response / inflammatory response / innate immune response / DNA damage response / mitochondrion / nucleoplasm / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Aequorea victoria (jellyfish) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 5.0 Å | |||||||||
Authors | Lu A / Li Y / Wu H | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9064.map.gz | 20.5 MB | EMDB map data format | |
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Header (meta data) | emd-9064-v30.xml emd-9064.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
Images | emd_9064.png | 70.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9064 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9064 | HTTPS FTP |
-Related structure data
Related structure data | 6mb2MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9064.map.gz / Format: CCP4 / Size: 112.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | PYD filament of AIM2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.575 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : PYD of AIM2
Entire | Name: PYD of AIM2 |
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Components |
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-Supramolecule #1: PYD of AIM2
Supramolecule | Name: PYD of AIM2 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Interferon-inducible protein AIM2
Macromolecule | Name: Interferon-inducible protein AIM2 / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 10.839629 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: AMESKYKEIL LLTGLDNITD EELDRFKGFL SDEFNIATGK LHTANRIQVA TLMIQNAGAV SAVMKTIRIF QKLNYMLLAK RLQEEKEKV DKQYK |
-Macromolecule #2: Green fluorescent protein
Macromolecule | Name: Green fluorescent protein / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO |
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Source (natural) | Organism: Aequorea victoria (jellyfish) |
Molecular weight | Theoretical: 25.924553 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | 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 ...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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 8 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: Solid cylinder |
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Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Applied 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 |