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- PDB-9u8k: Structure of ASC-PYD filament from condensates -

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Basic information

Entry
Database: PDB / ID: 9u8k
TitleStructure of ASC-PYD filament from condensates
ComponentsApoptosis-associated speck-like protein containing a CARD
KeywordsIMMUNE SYSTEM / ASC-PYD / filament / condensates
Function / homology
Function and homology information


CLEC7A/inflammasome pathway / The NLRP3 inflammasome / peptidase activator activity involved in apoptotic process / NLRP6 inflammasome complex / myosin I binding / Pyrin domain binding / myeloid dendritic cell activation involved in immune response / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / regulation of intrinsic apoptotic signaling pathway / myeloid dendritic cell activation ...CLEC7A/inflammasome pathway / The NLRP3 inflammasome / peptidase activator activity involved in apoptotic process / NLRP6 inflammasome complex / myosin I binding / Pyrin domain binding / myeloid dendritic cell activation involved in immune response / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / regulation of intrinsic apoptotic signaling pathway / myeloid dendritic cell activation / IkappaB kinase complex / AIM2 inflammasome complex / NLRP1 inflammasome complex / macropinocytosis / canonical inflammasome complex / interleukin-6 receptor binding / BMP receptor binding / NLRP3 inflammasome complex / NLRP3 inflammasome complex assembly / positive regulation of adaptive immune response / cysteine-type endopeptidase activator activity / negative regulation of interferon-beta production / regulation of tumor necrosis factor-mediated signaling pathway / regulation of GTPase activity / osmosensory signaling pathway / positive regulation of activated T cell proliferation / positive regulation of extrinsic apoptotic signaling pathway / pattern recognition receptor signaling pathway / pattern recognition receptor activity / tropomyosin binding / positive regulation of actin filament polymerization / positive regulation of release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of interleukin-10 production / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / pyroptotic inflammatory response / cellular response to interleukin-1 / positive regulation of T cell migration / positive regulation of defense response to virus by host / positive regulation of chemokine production / Neutrophil degranulation / negative regulation of cytokine production involved in inflammatory response / activation of innate immune response / intrinsic apoptotic signaling pathway / positive regulation of phagocytosis / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-1 beta production / regulation of autophagy / positive regulation of interleukin-8 production / negative regulation of canonical NF-kappaB signal transduction / response to bacterium / apoptotic signaling pathway / regulation of protein stability / positive regulation of non-canonical NF-kappaB signal transduction / protein homooligomerization / positive regulation of interleukin-6 production / positive regulation of JNK cascade / cellular response to tumor necrosis factor / positive regulation of type II interferon production / positive regulation of T cell activation / positive regulation of tumor necrosis factor production / positive regulation of inflammatory response / cellular response to lipopolysaccharide / regulation of inflammatory response / protease binding / regulation of apoptotic process / defense response to virus / defense response to Gram-negative bacterium / microtubule / transmembrane transporter binding / positive regulation of canonical NF-kappaB signal transduction / positive regulation of ERK1 and ERK2 cascade / protein dimerization activity / defense response to Gram-positive bacterium / positive regulation of apoptotic process / inflammatory response / Golgi membrane / innate immune response / neuronal cell body / apoptotic process / nucleolus / enzyme binding / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular region / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
CARD8/ASC/NALP1, CARD domain / : / DAPIN domain profile. / DAPIN domain / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily
Similarity search - Domain/homology
Apoptosis-associated speck-like protein containing a CARD
Similarity search - Component
Biological specieshuman gammaherpesvirus 4 (Epstein-Barr virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsGao, P. / Li, Q.J. / Li, Z.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Cell / Year: 2026
Title: DNA-triggered AIM2 condensation orchestrates immune activation and regulation.
Authors: Quanjin Li / Xiaohan Geng / Huiwen Yan / Zhaolong Li / Miao Shi / Ziqi Zhu / Tongxin Niu / Chunqiu Zhao / Kaile Shu / Yina Gao / Han Feng / Songqing Liu / Qiuyao Jiang / Pengcheng Bu / Dong Li / Pu Gao /
Abstract: The innate immune sensor AIM2 detects cytosolic DNA and initiates inflammatory responses, yet its activation mechanism remains incompletely understood. Here, we show that AIM2 undergoes liquid-liquid ...The innate immune sensor AIM2 detects cytosolic DNA and initiates inflammatory responses, yet its activation mechanism remains incompletely understood. Here, we show that AIM2 undergoes liquid-liquid phase separation upon DNA binding, forming dynamic condensates both in vitro and in cells. These condensates serve as platforms for inflammasome and PANoptosome assembly, promoting immune activation across multiple pathways. Direct structural determination from condensates reveals the assembly of active-form ASC filaments. Mechanistically, liquid-phase condensation is governed by multivalent interactions involving different AIM2 domains, including previously uncharacterized regions and species-specific elements. In vitro and in vivo assays show that mutants specifically disrupting condensation impair immune complex assembly, cell death initiation, antimicrobial defense, and intestinal homeostasis. Moreover, AIM2-DNA condensates function as regulatory hubs targeted by host- and pathogen-derived factors to balance immune homeostasis or facilitate immune evasion. These findings establish liquid-phase condensation as a fundamental mechanism of AIM2 activation and a potential therapeutic target.
History
DepositionMar 26, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apoptosis-associated speck-like protein containing a CARD
B: Apoptosis-associated speck-like protein containing a CARD
C: Apoptosis-associated speck-like protein containing a CARD
D: Apoptosis-associated speck-like protein containing a CARD
E: Apoptosis-associated speck-like protein containing a CARD
F: Apoptosis-associated speck-like protein containing a CARD
G: Apoptosis-associated speck-like protein containing a CARD
H: Apoptosis-associated speck-like protein containing a CARD
I: Apoptosis-associated speck-like protein containing a CARD
J: Apoptosis-associated speck-like protein containing a CARD
K: Apoptosis-associated speck-like protein containing a CARD
L: Apoptosis-associated speck-like protein containing a CARD
M: Apoptosis-associated speck-like protein containing a CARD
N: Apoptosis-associated speck-like protein containing a CARD
O: Apoptosis-associated speck-like protein containing a CARD
P: Apoptosis-associated speck-like protein containing a CARD
Q: Apoptosis-associated speck-like protein containing a CARD
R: Apoptosis-associated speck-like protein containing a CARD
S: Apoptosis-associated speck-like protein containing a CARD
T: Apoptosis-associated speck-like protein containing a CARD
U: Apoptosis-associated speck-like protein containing a CARD
V: Apoptosis-associated speck-like protein containing a CARD
W: Apoptosis-associated speck-like protein containing a CARD
X: Apoptosis-associated speck-like protein containing a CARD
Y: Apoptosis-associated speck-like protein containing a CARD
Z: Apoptosis-associated speck-like protein containing a CARD
a1: Apoptosis-associated speck-like protein containing a CARD
b1: Apoptosis-associated speck-like protein containing a CARD
c1: Apoptosis-associated speck-like protein containing a CARD
d1: Apoptosis-associated speck-like protein containing a CARD
e1: Apoptosis-associated speck-like protein containing a CARD
f1: Apoptosis-associated speck-like protein containing a CARD
g1: Apoptosis-associated speck-like protein containing a CARD
h1: Apoptosis-associated speck-like protein containing a CARD
i1: Apoptosis-associated speck-like protein containing a CARD
j1: Apoptosis-associated speck-like protein containing a CARD
k1: Apoptosis-associated speck-like protein containing a CARD
l1: Apoptosis-associated speck-like protein containing a CARD
m1: Apoptosis-associated speck-like protein containing a CARD


Theoretical massNumber of molelcules
Total (without water)450,34339
Polymers450,34339
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Apoptosis-associated speck-like protein containing a CARD / mASC / PYD and CARD domain-containing protein


Mass: 11547.250 Da / Num. of mol.: 39
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human gammaherpesvirus 4 (Epstein-Barr virus)
Production host: Escherichia coli (E. coli) / References: UniProt: Q9EPB4
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ASC-PYD filament from condensates / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS TITAN THEMIS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
9PHENIX1.19.2_4158model refinement
13cryoSPARC4.73D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45400 / Symmetry type: POINT

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