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- PDB-6n1i: Cryo-EM structure of NLRC4-CARD filament -

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Basic information

Entry
Database: PDB / ID: 6n1i
TitleCryo-EM structure of NLRC4-CARD filament
ComponentsNLR family CARD domain-containing protein 4
KeywordsSIGNALING PROTEIN / Inflammasome / filament / immunity
Function / homology
Function and homology information


IPAF inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / canonical inflammasome complex / caspase binding / positive regulation of protein processing / pattern recognition receptor signaling pathway / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response / endopeptidase activator activity ...IPAF inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / canonical inflammasome complex / caspase binding / positive regulation of protein processing / pattern recognition receptor signaling pathway / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response / endopeptidase activator activity / detection of bacterium / activation of innate immune response / positive regulation of interleukin-1 beta production / : / protein homooligomerization / positive regulation of inflammatory response / defense response to bacterium / positive regulation of apoptotic process / inflammatory response / innate immune response / intracellular membrane-bounded organelle / apoptotic process / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
NLR family CARD domain-containing protein 4 / NLRC4, helical domain / : / NLRC4 helical domain / Nlrc4-like, winged helix domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / CARD domain / CARD caspase recruitment domain profile. ...NLR family CARD domain-containing protein 4 / NLRC4, helical domain / : / NLRC4 helical domain / Nlrc4-like, winged helix domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NLR family CARD domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsLi, Y. / Fu, T. / Wu, H.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Cryo-EM structures of ASC and NLRC4 CARD filaments reveal a unified mechanism of nucleation and activation of caspase-1.
Authors: Yang Li / Tian-Min Fu / Alvin Lu / Kristen Witt / Jianbin Ruan / Chen Shen / Hao Wu /
Abstract: Canonical inflammasomes are cytosolic supramolecular complexes that activate caspase-1 upon sensing extrinsic microbial invasions and intrinsic sterile stress signals. During inflammasome assembly, ...Canonical inflammasomes are cytosolic supramolecular complexes that activate caspase-1 upon sensing extrinsic microbial invasions and intrinsic sterile stress signals. During inflammasome assembly, adaptor proteins ASC and NLRC4 recruit caspase-1 through homotypic caspase recruitment domain (CARD) interactions, leading to caspase-1 dimerization and activation. Activated caspase-1 processes proinflammatory cytokines and Gasdermin D to induce cytokine maturation and pyroptotic cell death. Here, we present cryo-electron microscopy (cryo-EM) structures of NLRC4 CARD and ASC CARD filaments mediated by conserved three types of asymmetric interactions (types I, II, and III). We find that the CARDs of these two adaptor proteins share a similar assembly pattern, which matches that of the caspase-1 CARD filament whose structure we defined previously. These data indicate a unified mechanism for downstream caspase-1 recruitment through CARD-CARD interactions by both adaptors. Using structure modeling, we further show that full-length NLRC4 assembles via two separate symmetries at its CARD and its nucleotide-binding domain (NBD), respectively.
History
DepositionNov 8, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionDec 5, 2018ID: 6DRP
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 28, 2025Group: Data collection / Structure summary / Category: em_software / pdbx_entry_details / Item: _em_software.name

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Assembly

Deposited unit
A: NLR family CARD domain-containing protein 4
B: NLR family CARD domain-containing protein 4
C: NLR family CARD domain-containing protein 4
D: NLR family CARD domain-containing protein 4
E: NLR family CARD domain-containing protein 4
F: NLR family CARD domain-containing protein 4
G: NLR family CARD domain-containing protein 4
H: NLR family CARD domain-containing protein 4
I: NLR family CARD domain-containing protein 4
J: NLR family CARD domain-containing protein 4
K: NLR family CARD domain-containing protein 4
L: NLR family CARD domain-containing protein 4
M: NLR family CARD domain-containing protein 4
N: NLR family CARD domain-containing protein 4
O: NLR family CARD domain-containing protein 4
P: NLR family CARD domain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)159,80316
Polymers159,80316
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area31960 Å2
ΔGint-54 kcal/mol
Surface area51290 Å2
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 16 / Rise per n subunits: 4.93 Å / Rotation per n subunits: -100.48 °)

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Components

#1: Protein
NLR family CARD domain-containing protein 4 / CARD / LRR / and NACHT-containing protein / Clan protein / Caspase recruitment domain-containing ...CARD / LRR / and NACHT-containing protein / Clan protein / Caspase recruitment domain-containing protein 12 / Ice protease-activating factor / Ipaf


Mass: 9987.671 Da / Num. of mol.: 16 / Fragment: CARD (UNP residues 1-85)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLRC4, CARD12, CLAN, CLAN1, IPAF, UNQ6189/PRO20215 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NPP4
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: NLRC4-CARD filament / Type: CELL / 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: 41 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -100.48 ° / Axial rise/subunit: 4.93 Å / Axial symmetry: C1
3D reconstructionResolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 199312 / Symmetry type: HELICAL

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