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- PDB-6mb2: Cryo-EM structure of the PYD filament of AIM2 -

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Basic information

Entry
Database: PDB / ID: 6mb2
TitleCryo-EM structure of the PYD filament of AIM2
Components
  • Green fluorescent protein
  • Interferon-inducible protein AIM2
KeywordsIMMUNE 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 / 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 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 / Green fluorescent protein, GFP / Death-like domain superfamily ...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 / 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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 5 Å
AuthorsLu, A. / Li, Y. / Wu, H.
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, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Interferon-inducible protein AIM2
B: Interferon-inducible protein AIM2
C: Interferon-inducible protein AIM2
D: Interferon-inducible protein AIM2
E: Interferon-inducible protein AIM2
F: Interferon-inducible protein AIM2
G: Interferon-inducible protein AIM2
H: Interferon-inducible protein AIM2
I: Interferon-inducible protein AIM2
J: Interferon-inducible protein AIM2
K: Interferon-inducible protein AIM2
L: Interferon-inducible protein AIM2
M: Interferon-inducible protein AIM2
N: Interferon-inducible protein AIM2
O: Interferon-inducible protein AIM2
a: Green fluorescent protein
b: Green fluorescent protein
c: Green fluorescent protein
d: Green fluorescent protein
e: Green fluorescent protein
f: Green fluorescent protein
g: Green fluorescent protein
h: Green fluorescent protein
i: Green fluorescent protein
j: Green fluorescent protein
k: Green fluorescent protein
l: Green fluorescent protein
m: Green fluorescent protein
n: Green fluorescent protein
o: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)551,46330
Polymers551,46330
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
SymmetryHelical 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 °)

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Components

#1: Protein
Interferon-inducible protein AIM2 / Absent in melanoma 2


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
Green fluorescent 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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: PYD of AIM2 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.8.2_1309 / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 138.9 ° / Axial rise/subunit: 6 Å / Axial symmetry: C1
3D reconstructionResolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54973 / Symmetry type: HELICAL
RefinementResolution: 5→150 Å / SU ML: 1.77 / σ(F): 0.76 / Phase error: 64.53 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.4227 2688 4.77 %
Rwork0.3574 --
obs0.3606 56399 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0111190
ELECTRON MICROSCOPYf_angle_d0.9115045
ELECTRON MICROSCOPYf_dihedral_angle_d14.174200
ELECTRON MICROSCOPYf_chiral_restr0.0311785
ELECTRON MICROSCOPYf_plane_restr0.0041920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5-5.09090.45931920.44272742ELECTRON MICROSCOPY100
5.0909-5.18880.43841080.43312955ELECTRON MICROSCOPY100
5.1888-5.29480.48111200.45152820ELECTRON MICROSCOPY100
5.2948-5.40990.53052640.53132847ELECTRON MICROSCOPY100
5.4099-5.53570.56212040.51892476ELECTRON MICROSCOPY100
5.5357-5.67420.55871440.50382970ELECTRON MICROSCOPY100
5.6742-5.82760.5113960.51032790ELECTRON MICROSCOPY100
5.8276-5.99910.56111670.51762994ELECTRON MICROSCOPY100
5.9991-6.19270.5967840.49472752ELECTRON MICROSCOPY100
6.1927-6.41410.4892960.49252874ELECTRON MICROSCOPY100
6.4141-6.67090.59121340.50752938ELECTRON MICROSCOPY100
6.6709-6.97450.4672960.48522724ELECTRON MICROSCOPY100
6.9745-7.34220.5433720.49022988ELECTRON MICROSCOPY100
7.3422-7.80220.50111680.50242841ELECTRON MICROSCOPY100
7.8022-8.40450.53211320.42142796ELECTRON MICROSCOPY100
8.4045-9.25020.45531230.37712878ELECTRON MICROSCOPY100
9.2502-10.58840.34871650.34532821ELECTRON MICROSCOPY99
10.5884-13.3390.28411540.28952710ELECTRON MICROSCOPY99
13.339-150.06750.38091690.20282795ELECTRON MICROSCOPY98

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