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- EMDB-6458: Cryo-EM Structure of the Activated NAIP2/NLRC4 Inflammasome Revea... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6458 | |||||||||
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Title | Cryo-EM Structure of the Activated NAIP2/NLRC4 Inflammasome Reveals Nucleated Polymerization | |||||||||
![]() | Reconstruction of 11-fold NAIP2/NLRC4 inflammasome | |||||||||
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![]() | Inflammasome / NLRC4 / NAIP2 | |||||||||
Function / homology | ![]() IPAF inflammasome complex / pyroptotic inflammatory response / detection of bacterium / activation of innate immune response / positive regulation of interleukin-1 beta production / protein homooligomerization / regulation of apoptotic process / defense response to bacterium / inflammatory response / innate immune response ...IPAF inflammasome complex / pyroptotic inflammatory response / detection of bacterium / activation of innate immune response / positive regulation of interleukin-1 beta production / protein homooligomerization / regulation of apoptotic process / defense response to bacterium / inflammatory response / innate immune response / apoptotic process / protein homodimerization activity / ATP binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||
![]() | Zhang L / Chen S / Ruan J / Wu J / Tong AB / Yin Q / Li Y / David L / Lu A / Wang WL ...Zhang L / Chen S / Ruan J / Wu J / Tong AB / Yin Q / Li Y / David L / Lu A / Wang WL / Marks C / Ouyang Q / Zhang X / Mao Y / Wu H | |||||||||
![]() | ![]() Title: Cryo-EM structure of the activated NAIP2-NLRC4 inflammasome reveals nucleated polymerization. Authors: Liman Zhang / Shuobing Chen / Jianbin Ruan / Jiayi Wu / Alexander B Tong / Qian Yin / Yang Li / Liron David / Alvin Lu / Wei Li Wang / Carolyn Marks / Qi Ouyang / Xinzheng Zhang / Youdong Mao / Hao Wu / ![]() ![]() Abstract: The NLR family apoptosis inhibitory proteins (NAIPs) bind conserved bacterial ligands, such as the bacterial rod protein PrgJ, and recruit NLR family CARD-containing protein 4 (NLRC4) as the ...The NLR family apoptosis inhibitory proteins (NAIPs) bind conserved bacterial ligands, such as the bacterial rod protein PrgJ, and recruit NLR family CARD-containing protein 4 (NLRC4) as the inflammasome adapter to activate innate immunity. We found that the PrgJ-NAIP2-NLRC4 inflammasome is assembled into multisubunit disk-like structures through a unidirectional adenosine triphosphatase polymerization, primed with a single PrgJ-activated NAIP2 per disk. Cryo-electron microscopy (cryo-EM) reconstruction at subnanometer resolution revealed a ~90° hinge rotation accompanying NLRC4 activation. Unlike in the related heptameric Apaf-1 apoptosome, in which each subunit needs to be conformationally activated by its ligand before assembly, a single PrgJ-activated NAIP2 initiates NLRC4 polymerization in a domino-like reaction to promote the disk assembly. These insights reveal the mechanism of signal amplification in NAIP-NLRC4 inflammasomes. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 313.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.2 KB 13.2 KB | Display Display | ![]() |
Images | ![]() | 322.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3jblMC ![]() 6459C ![]() 6460C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 1.7 TB Data #1: Drift-corrected micrographs of NLRC4/NAIP2 inflammasome [micrographs - single frame] Data #2: Single-particle stacks of NLRC4/NAIP2 inflammasome [picked particles - multiframe - processed]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Reconstruction of 11-fold NAIP2/NLRC4 inflammasome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : NAIP2/NLRC4 inflammasome, 11-fold disk
Entire | Name: NAIP2/NLRC4 inflammasome, 11-fold disk |
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Components |
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-Supramolecule #1000: NAIP2/NLRC4 inflammasome, 11-fold disk
Supramolecule | Name: NAIP2/NLRC4 inflammasome, 11-fold disk / type: sample / ID: 1000 Details: The sample contains multiple oligomeric states, including 10-fold, 11-fold, and 12-fold disks. Oligomeric state: One NAIP2 subunit and ten NLRC subunits / Number unique components: 2 |
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Molecular weight | Experimental: 1.8 MDa / Theoretical: 1.8 MDa |
-Macromolecule #1: NLR family CARD domain-containing protein 4
Macromolecule | Name: NLR family CARD domain-containing protein 4 / type: protein_or_peptide / ID: 1 / Name.synonym: NLRC4 Details: One activated NAIP2 induces polymerization of NLRC4. Number of copies: 10 Oligomeric state: NLRC4 inflammasome comprises ten NLRC4 and one NAIP2 Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() Tissue: Abelson murine leukemia virus-induced tumor; ascites Cell: macrophage / Location in cell: cytosol |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: NLR family CARD domain-containing protein 4 |
-Macromolecule #2: NLR family, apoptosis inhibitory protein 2
Macromolecule | Name: NLR family, apoptosis inhibitory protein 2 / type: protein_or_peptide / ID: 2 / Name.synonym: NAIP2 Details: One activated NAIP2 induces polymerization of NLRC4. Number of copies: 1 Oligomeric state: NLRC4 inflammasome comprises one NAIP2 and ten NLRC4 Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() Tissue: Abelson murine leukemia virus-induced tumor; ascites Cell: macrophage / Location in cell: cytosol |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 8 / Details: 25 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM DTT |
Grid | Details: 400 mesh C-flat grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 103 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for one second before plunging |
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Electron microscopy
Microscope | OTHER |
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Temperature | Min: 79.5 K / Max: 80 K / Average: 79.5 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 21,000 times magnification. |
Date | Apr 1, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 5 µm / Number real images: 9113 / Average electron dose: 48 e/Å2 Details: average of 36 frames recorded by the direct electron detector Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 28736 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 21000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
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Image processing
CTF correction | Details: Wiener-type filter |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: OTHER / Software - Name: Spider, EMAN2, Relion / Number images used: 75114 |