+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9946 | |||||||||
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Title | Structure of NLRC4 CARD filament | |||||||||
Map data | None | |||||||||
Sample |
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Keywords | filament / SIGNALING PROTEIN | |||||||||
Function / homology | Function and homology information The IPAF inflammasome / IPAF inflammasome complex / icosanoid biosynthetic process / canonical inflammasome complex / positive regulation of protein processing / caspase binding / activation of cysteine-type endopeptidase activity / pattern recognition receptor signaling pathway / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response ...The IPAF inflammasome / IPAF inflammasome complex / icosanoid biosynthetic process / canonical inflammasome complex / positive regulation of protein processing / caspase binding / activation of cysteine-type endopeptidase activity / 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 / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of NF-kappaB transcription factor activity / defense response to bacterium / inflammatory response / positive regulation of apoptotic process / intracellular membrane-bounded organelle / innate immune response / apoptotic process / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Gong Q / Xu C | |||||||||
Funding support | Singapore, 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis for distinct inflammasome complex assembly by human NLRP1 and CARD8. Authors: Qin Gong / Kim Robinson / Chenrui Xu / Phuong Thao Huynh / Kelvin Han Chung Chong / Eddie Yong Jun Tan / Jiawen Zhang / Zhao Zhi Boo / Daniel Eng Thiam Teo / Kenneth Lay / Yaming Zhang / ...Authors: Qin Gong / Kim Robinson / Chenrui Xu / Phuong Thao Huynh / Kelvin Han Chung Chong / Eddie Yong Jun Tan / Jiawen Zhang / Zhao Zhi Boo / Daniel Eng Thiam Teo / Kenneth Lay / Yaming Zhang / John Soon Yew Lim / Wah Ing Goh / Graham Wright / Franklin L Zhong / Bruno Reversade / Bin Wu / Abstract: Nod-like receptor (NLR) proteins activate pyroptotic cell death and IL-1 driven inflammation by assembling and activating the inflammasome complex. Closely related sensor proteins NLRP1 and CARD8 ...Nod-like receptor (NLR) proteins activate pyroptotic cell death and IL-1 driven inflammation by assembling and activating the inflammasome complex. Closely related sensor proteins NLRP1 and CARD8 undergo unique auto-proteolysis-dependent activation and are implicated in auto-inflammatory diseases; however, their mechanisms of activation are not understood. Here we report the structural basis of how the activating domains (FIIND-CARD) of NLRP1 and CARD8 self-oligomerize to assemble distinct inflammasome complexes. Recombinant FIIND-CARD of NLRP1 forms a two-layered filament, with an inner core of oligomerized CARD surrounded by an outer ring of FIIND. Biochemically, self-assembled NLRP1-CARD filaments are sufficient to drive ASC speck formation in cultured human cells-a process that is greatly enhanced by NLRP1-FIIND which forms oligomers in vitro. The cryo-EM structures of NLRP1-CARD and CARD8-CARD filaments, solved here at 3.7 Å, uncover unique structural features that enable NLRP1 and CARD8 to discriminate between ASC and pro-caspase-1. In summary, our findings provide structural insight into the mechanisms of activation for human NLRP1 and CARD8 and reveal how highly specific signaling can be achieved by heterotypic CARD interactions within the inflammasome complexes. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9946.map.gz | 2.3 MB | EMDB map data format | |
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Header (meta data) | emd-9946-v30.xml emd-9946.xml | 18 KB 18 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9946_fsc.xml | 3.7 KB | Display | FSC data file |
Images | emd_9946.png | 72.2 KB | ||
Filedesc metadata | emd-9946.cif.gz | 5.8 KB | ||
Others | emd_9946_additional.map.gz emd_9946_half_map_1.map.gz emd_9946_half_map_2.map.gz | 579.1 KB 2.4 MB 2.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9946 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9946 | HTTPS FTP |
-Validation report
Summary document | emd_9946_validation.pdf.gz | 827.4 KB | Display | EMDB validaton report |
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Full document | emd_9946_full_validation.pdf.gz | 827 KB | Display | |
Data in XML | emd_9946_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | emd_9946_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9946 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9946 | HTTPS FTP |
-Related structure data
Related structure data | 6k8jMC 9943C 9947C 9948C 6k7vC 6k99C 6k9fC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9946.map.gz / Format: CCP4 / Size: 2.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: cropped 12mer from filament, used for model alignment...
File | emd_9946_additional.map | ||||||||||||
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Annotation | cropped 12mer from filament, used for model alignment and refinement, not for publication | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: None
File | emd_9946_half_map_1.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: None
File | emd_9946_half_map_2.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : NLRC4 CARD filament
Entire | Name: NLRC4 CARD filament |
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Components |
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-Supramolecule #1: NLRC4 CARD filament
Supramolecule | Name: NLRC4 CARD filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: NLR family CARD domain-containing protein 4
Macromolecule | Name: NLR family CARD domain-containing protein 4 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.600412 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: GPGVDEALRE AQTKSAMNFI KDNSRALIQR MGMTVIKQIT DDLFVWNVLN REEVNIICCE KVEQDAARGI IHMILKKGSE SCNLFLKSL KEWNYPLFQD LN UniProtKB: NLR family CARD domain-containing protein 4 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 8 |
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Grid | Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 2109 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-6k8j: |