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- PDB-9wz6: Full-length Caspase-1-CARD filament -

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Basic information

Entry
Database: PDB / ID: 9wz6
TitleFull-length Caspase-1-CARD filament
ComponentsCaspase-1
KeywordsIMMUNE SYSTEM / filament / PYD / CARD
Function / homology
Function and homology information


caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / IPAF inflammasome complex / The AIM2 inflammasome / AIM2 inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / NLRP1 inflammasome complex / canonical inflammasome complex ...caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / IPAF inflammasome complex / The AIM2 inflammasome / AIM2 inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / NLRP1 inflammasome complex / canonical inflammasome complex / positive regulation of interleukin-18 production / CARD domain binding / cytokine precursor processing / NLRP3 inflammasome complex / Interleukin-1 processing / osmosensory signaling pathway / Interleukin-37 signaling / positive regulation of tumor necrosis factor-mediated signaling pathway / pattern recognition receptor signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process / signaling receptor ligand precursor processing / TP53 Regulates Transcription of Caspase Activators and Caspases / cytokine binding / pyroptotic inflammatory response / protein autoprocessing / The NLRP3 inflammasome / Pyroptosis / Purinergic signaling in leishmaniasis infection / protein maturation / positive regulation of interleukin-1 beta production / cellular response to mechanical stimulus / NOD1/2 Signaling Pathway / cellular response to type II interferon / kinase binding / positive regulation of inflammatory response / SARS-CoV-1 activates/modulates innate immune responses / cellular response to lipopolysaccharide / regulation of inflammatory response / regulation of apoptotic process / endopeptidase activity / defense response to virus / microtubule / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / nucleolus / signal transduction / protein-containing complex / proteolysis / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. ...Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsXue, D. / Ni, F. / Liu, S. / Yan, H. / Luo, Z. / Fu, G. / Wang, Q. / Ma, J.
Funding support China, 3items
OrganizationGrant numberCountry
Other governmentNational Key Research and Development Program of China (No. 2024YFA1307502) China
Other governmentScience and Technology Innovation Plan of Shanghai Science and Technology Commission (No. 23JS1400200) China
Other governmentResearch Fund for International Senior Scientists (No. W2431060) China
CitationJournal: Nat Commun / Year: 2025
Title: Atomic mechanisms of full-length ASC-mediated inflammasome assembly.
Authors: Dongmei Xue / Fengyun Ni / Sheng Liu / Huifang Yan / Zhenwei Luo / Gang Fu / Qinghua Wang / Jianpeng Ma /
Abstract: ASC (Apoptosis-associated Speck-like protein containing a CARD) is a key adaptor protein that assembles inflammasomes by linking sensors such as NLRP3 to effectors like Caspase-1 via its PYD and CARD ...ASC (Apoptosis-associated Speck-like protein containing a CARD) is a key adaptor protein that assembles inflammasomes by linking sensors such as NLRP3 to effectors like Caspase-1 via its PYD and CARD Death Domains. Due to ASC's propensity to self-aggregate, most high-resolution structural studies focused on isolated PYD or CARD domains, leaving the atomic basis of full-length ASC assembly unknown. Here we determine atomic-resolution cryo-EM structures of PYD and CARD filaments from full-length ASC, revealing characteristic multitrack bundles composed of alternating ASC and ASC filaments that expose multiple interfaces for flexible assembly and efficient signaling. We further show that Caspase-1 filaments nucleate specifically from the B-end of ASC filaments, and that the interdomain linker modulates bundle formation. The ASC isoform ASCb, with a four-residue linker, adopts a distinct architecture, correlating with reduced Caspase-1 activation efficiency. In ASC THP-1 cells, only wild-type ASC, not interface-disrupting mutants, restored ASC speck formation and Caspase-1 activation, underscoring the requirement for intact multitrack bundles. Cryo-electron tomography captures snapshots of higher-order inflammasome structures. These findings collectively define the structural and functional principles by which ASC organizes inflammasomes to amplify immune signaling.
History
DepositionSep 29, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-1
B: Caspase-1
C: Caspase-1
D: Caspase-1
E: Caspase-1
F: Caspase-1
G: Caspase-1
H: Caspase-1


Theoretical massNumber of molelcules
Total (without water)361,7088
Polymers361,7088
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
Caspase-1 / Full-length Cascade-1 CARD filament / CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin- ...Full-length Cascade-1 CARD filament / CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / ICE / IL-1 beta-converting enzyme / p45


Mass: 45213.551 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Production host: Homo sapiens (human) / References: UniProt: P29466, caspase-1
Has protein modificationN

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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: Filament / Type: CELL / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.19.2_4158model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -100.2 ° / Axial rise/subunit: 5.1 Å / Axial symmetry: C3
3D reconstructionResolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1565512 / Symmetry type: HELICAL
RefinementHighest resolution: 2.66 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025568
ELECTRON MICROSCOPYf_angle_d0.4187440
ELECTRON MICROSCOPYf_dihedral_angle_d4.07760
ELECTRON MICROSCOPYf_chiral_restr0.034896
ELECTRON MICROSCOPYf_plane_restr0.003936

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