|Entry||Database: EMDB / ID: 9137|
|Title||Cryo-EM structure of NLRC4-CARD filament|
|Function / homology||Caspase recruitment domain / Green fluorescent protein / Green fluorescent protein / NACHT domain / CARD caspase recruitment domain profile. / Green fluorescent protein, GFP / CARD domain / NACHT nucleoside triphosphatase / Death-like domain superfamily / Green fluorescent protein-related ...Caspase recruitment domain / Green fluorescent protein / Green fluorescent protein / NACHT domain / CARD caspase recruitment domain profile. / Green fluorescent protein, GFP / CARD domain / NACHT nucleoside triphosphatase / Death-like domain superfamily / Green fluorescent protein-related / NACHT-NTPase domain profile. / TP53 Regulates Transcription of Caspase Activators and Caspases / P-loop containing nucleoside triphosphate hydrolase / The IPAF inflammasome / Leucine-rich repeat domain superfamily / interleukin-1 beta secretion / IPAF inflammasome complex / pyroptosis / inhibition of cysteine-type endopeptidase activity involved in apoptotic process / detection of bacterium / activation of innate immune response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / regulation of signal transduction / bioluminescence / generation of precursor metabolites and energy / activation of cysteine-type endopeptidase activity involved in apoptotic process / ubiquitin-protein transferase activity / protein homooligomerization / regulation of apoptotic process / positive regulation of NF-kappaB transcription factor activity / inflammatory response / positive regulation of apoptotic process / intracellular / defense response to bacterium / innate immune response / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / nucleus / cytosol / EGFP / NLR family CARD domain-containing protein 4|
Function and homology information
|Source||Homo sapiens (human) / Vaccinia virus|
|Method||helical reconstruction / cryo EM / 3.4 Å resolution|
|Authors||Zheng W / Matyszewski M / Sohn J / Egelman EH|
|Citation||Journal: J. Biol. Chem. / Year: 2018|
Title: Cryo-EM structure of the NLRC4 filament provides insights into how symmetric and asymmetric supramolecular structures drive inflammasome assembly.
Authors: Mariusz Matyszewski / Weili Zheng / Jacob Lueck / Brendan Antiochos / Edward H Egelman / Jungsan Sohn
Abstract: Inflammasomes are supramolecular signaling platforms integral to innate immune defense against invading pathogens. The Nod Like Receptor (NLR) family apoptosis inhibitory protein (NAIP)•NLR family ...Inflammasomes are supramolecular signaling platforms integral to innate immune defense against invading pathogens. The Nod Like Receptor (NLR) family apoptosis inhibitory protein (NAIP)•NLR family caspase-recruiting domain (CARD) domain-containing 4 (NLRC4) inflammasome recognizes intracellular bacteria and induces the polymerization of the caspase-1 protease, which in turn executes maturation of interleukin-1β (IL-1β) and pyroptosis. Several high-resolution structures of the fully assembled NAIP•NLRC4 complex are available, but these structures do not resolve the architecture of the CARD filament in atomic detail. Here, we present the cryo-EM structure of the filament assembled by the CARD of human NLRC4 (NLRC4) at 3.4 Å resolution. The structure revealed that the helical architecture of the NLRC4 filament is essentially identical to that of the downstream filament assembled by the CARD of caspase-1 (casp1), but deviates from the split washer-like assembly of the NAIP•NLRC4 oligomer. Our results suggest that architectural complementarity is a major driver for the recognition between up- and downstream CARD assemblies in inflammasomes. Furthermore, a Monte Carlo simulation of the NLRC4 filament assembly rationalizes why an (un)decameric NLRC4 oligomer is optimal for assembling the helical base of the NLRC4 filament. Together, our results explain how symmetric and asymmetric supramolecular assemblies enable high-fidelity signaling in inflammasomes.
|Validation Report||PDB-ID: 6mks|
SummaryFull reportAbout validation report
|Date||Deposition: Sep 26, 2018 / Header (metadata) release: Oct 3, 2018 / Map release: Nov 7, 2018 / Last update: Nov 14, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_9137.map.gz (map file in CCP4 format, 8389 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.32 Å|
CCP4 map header:
-Entire NLRC4-CARD filament
|Entire||Name: NLRC4-CARD filament / Number of components: 2|
-Component #1: protein, NLRC4-CARD filament
|Protein||Name: NLRC4-CARD filament / Recombinant expression: No|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Escherichia coli BL21(DE3) (bacteria) / Vector: pET21b|
-Component #2: protein, Chimera protein of NLR family CARD domain-containing pro...
|Protein||Name: Chimera protein of NLR family CARD domain-containing protein 4 and EGFP|
Number of Copies: 31 / Recombinant expression: No
|Mass||Theoretical: 38.668805 kDa|
|Source||Species: Vaccinia virus|
|Source (engineered)||Expression System: Escherichia coli BL21(DE3) (bacteria)|
|Specimen||Specimen state: filament / Method: cryo EM|
|Helical parameters||Axial symmetry: C1 (asymmetric) / Delta z: 5 Å / Delta phi: 100.6 deg.|
|Sample solution||Buffer solution: 20mM HEPES at pH 7.4, 400mM NaCl, 10% glycerol, 1mM EDTA and 1mM DTT|
|Vitrification||Cryogen name: ETHANE / Humidity: 100 %|
-Electron microscopy imaging
|Imaging||Microscope: FEI TITAN|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 42 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Cs: 2.7 mm / Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 1690|
|Processing||Method: helical reconstruction|
|3D reconstruction||Algorithm: BACK PROJECTION / Software: SPIDER / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
-Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi