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- PDB-7k3r: Cryo-EM structure of AIM2-PYD filament -

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Basic information

Entry
Database: PDB / ID: 7k3r
TitleCryo-EM structure of AIM2-PYD filament
ComponentsInterferon-inducible protein AIM2
KeywordsPROTEIN FIBRIL / Inflammasome / AIM2 filament / Helical reconstruction
Function / homology
Function and homology information


pyroptosome complex assembly / AIM2 inflammasome complex assembly / The AIM2 inflammasome / cysteine-type endopeptidase activator activity / regulation of behavior / AIM2 inflammasome complex / 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 / regulation of behavior / AIM2 inflammasome complex / 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 / 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 / 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
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 / Death-like domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Interferon-inducible protein AIM2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZheng, W. / Matyszewski, M. / Sohn, J. / Egelman, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
CitationJournal: 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
DepositionSep 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-22656
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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
P: Interferon-inducible protein AIM2
Q: Interferon-inducible protein AIM2
R: Interferon-inducible protein AIM2
S: Interferon-inducible protein AIM2
T: Interferon-inducible protein AIM2
U: Interferon-inducible protein AIM2


Theoretical massNumber of molelcules
Total (without water)284,10221
Polymers284,10221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area33310 Å2
ΔGint-108 kcal/mol
Surface area86510 Å2
SymmetryHelical symmetry: (Circular symmetry: 3 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 7 / Rise per n subunits: 14 Å / Rotation per n subunits: 53.3 °)

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Components

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


Mass: 13528.655 Da / Num. of mol.: 21
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIM2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14862

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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: AIM2-PYD filament / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
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
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_2471: / Classification: refinement
EM software
IDNameVersionCategory
1EMAN2particle selection
4CTFFIND3CTF correction
7UCSF Chimeramodel fitting
9SPIDERinitial Euler assignment
12SPIDER3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 53.3 ° / Axial rise/subunit: 14 Å / Axial symmetry: C3
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99237 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00616359
ELECTRON MICROSCOPYf_angle_d0.70121861
ELECTRON MICROSCOPYf_dihedral_angle_d3.83710185
ELECTRON MICROSCOPYf_chiral_restr0.0462520
ELECTRON MICROSCOPYf_plane_restr0.0032751

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