+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22656 | |||||||||
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Title | Cryo-EM structure of AIM2-PYD filament | |||||||||
Map data | Cryo-EM structure of AIM2-PYD filament | |||||||||
Sample |
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Keywords | Inflammasome / 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 / AIM2 inflammasome complex / regulation of behavior / 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 / AIM2 inflammasome complex / regulation of behavior / 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 / cellular response to interferon-beta / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Zheng W / Matyszewski M | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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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_22656.map.gz | 20 MB | EMDB map data format | |
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Header (meta data) | emd-22656-v30.xml emd-22656.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
Images | emd_22656.png | 149.7 KB | ||
Filedesc metadata | emd-22656.cif.gz | 5.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22656 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22656 | HTTPS FTP |
-Validation report
Summary document | emd_22656_validation.pdf.gz | 526.9 KB | Display | EMDB validaton report |
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Full document | emd_22656_full_validation.pdf.gz | 526.4 KB | Display | |
Data in XML | emd_22656_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | emd_22656_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22656 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22656 | HTTPS FTP |
-Related structure data
Related structure data | 7k3rMC 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_22656.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of AIM2-PYD filament | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.66 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 : AIM2-PYD filament
Entire | Name: AIM2-PYD filament |
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Components |
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-Supramolecule #1: AIM2-PYD filament
Supramolecule | Name: AIM2-PYD filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Interferon-inducible protein AIM2
Macromolecule | Name: Interferon-inducible protein AIM2 / type: protein_or_peptide / ID: 1 / Number of copies: 21 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.528655 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GTGMESKYKE ILLLTGLDNI TDEELDRFKF FLSDEFNIAT GKLHTANRIQ VATLMIQNAG AVSAVMKTIR IFQKLNYMLL AKRLQEEKE KVDKQYKSVT KPKPLSQAEM SPAASAAIRN D UniProtKB: Interferon-inducible protein AIM2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Pretreatment - Type: PLASMA CLEANING / Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied 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 |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Final angle assignment | Type: NOT APPLICABLE |