+Open data
-Basic information
Entry | Database: PDB / ID: 6mb2 | ||||||
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Title | Cryo-EM structure of the PYD filament of AIM2 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Filament / higher order / innate immunity / inflammasome | ||||||
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 / positive regulation of interleukin-1 beta production / generation of precursor metabolites and energy / 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 | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 5 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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6mb2.cif.gz | 910.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mb2.ent.gz | 775.2 KB | Display | PDB format |
PDBx/mmJSON format | 6mb2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/6mb2 ftp://data.pdbj.org/pub/pdb/validation_reports/mb/6mb2 | HTTPS FTP |
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-Related structure data
Related structure data | 9064MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 15 / Rise per n subunits: 6 Å / Rotation per n subunits: 138.9 °) |
-Components
#1: Protein | Mass: 10839.629 Da / Num. of mol.: 15 / Fragment: PYD (UNP residues 1-93) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AIM2 / Production host: Escherichia coli (E. coli) / References: UniProt: O14862 #2: Protein | Mass: 25924.553 Da / Num. of mol.: 15 / Fragment: UNP residues 2-229 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: PYD of AIM2 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.8.2_1309 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 138.9 ° / Axial rise/subunit: 6 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54973 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 5→150 Å / SU ML: 1.77 / σ(F): 0.76 / Phase error: 64.53 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell |
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