+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9943 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of NLRP1 CARD filament | |||||||||
Map data | None | |||||||||
Sample |
| |||||||||
Keywords | filament / SIGNALING PROTEIN | |||||||||
Function / homology | Function and homology information NLRP1 inflammasome complex assembly / cysteine-type endopeptidase activator activity / NLRP1 inflammasome complex / canonical inflammasome complex / The NLRP1 inflammasome / self proteolysis / Hydrolases; Acting on peptide bonds (peptidases) / pattern recognition receptor signaling pathway / pattern recognition receptor activity / cellular response to UV-B ...NLRP1 inflammasome complex assembly / cysteine-type endopeptidase activator activity / NLRP1 inflammasome complex / canonical inflammasome complex / The NLRP1 inflammasome / self proteolysis / Hydrolases; Acting on peptide bonds (peptidases) / pattern recognition receptor signaling pathway / pattern recognition receptor activity / cellular response to UV-B / pyroptotic inflammatory response / cysteine-type endopeptidase activator activity involved in apoptotic process / response to muramyl dipeptide / antiviral innate immune response / signaling adaptor activity / molecular condensate scaffold activity / positive regulation of interleukin-1 beta production / : / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein homooligomerization / positive regulation of inflammatory response / activation of cysteine-type endopeptidase activity involved in apoptotic process / double-stranded RNA binding / peptidase activity / regulation of inflammatory response / double-stranded DNA binding / regulation of apoptotic process / neuron apoptotic process / defense response to virus / defense response to bacterium / protein domain specific binding / apoptotic process / nucleolus / enzyme binding / signal transduction / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Qin G / Chenrui X | |||||||||
Funding support | Singapore, 1 items
| |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9943.map.gz | 4.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-9943-v30.xml emd-9943.xml | 18 KB 18 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9943_fsc.xml | 4.6 KB | Display | FSC data file |
Images | emd_9943.png | 63.4 KB | ||
Filedesc metadata | emd-9943.cif.gz | 5.8 KB | ||
Others | emd_9943_additional.map.gz emd_9943_half_map_1.map.gz emd_9943_half_map_2.map.gz | 626.9 KB 4.4 MB 4.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9943 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9943 | HTTPS FTP |
-Validation report
Summary document | emd_9943_validation.pdf.gz | 836.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_9943_full_validation.pdf.gz | 835.8 KB | Display | |
Data in XML | emd_9943_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | emd_9943_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9943 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9943 | HTTPS FTP |
-Related structure data
Related structure data | 6k7vMC 9946C 9947C 9948C 6k8jC 6k99C 6k9fC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_9943.map.gz / Format: CCP4 / Size: 5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: cropped out 12mer density used in qseudo-crystallographic refinement,...
File | emd_9943_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | cropped out 12mer density used in qseudo-crystallographic refinement, not for publication. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_9943_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_9943_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : NLRP1 CARD filament
Entire | Name: NLRP1 CARD filament |
---|---|
Components |
|
-Supramolecule #1: NLRP1 CARD filament
Supramolecule | Name: NLRP1 CARD filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: NACHT, LRR and PYD domains-containing protein 1
Macromolecule | Name: NACHT, LRR and PYD domains-containing protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.203776 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: GPGDYKDDDD KDAPQLLHFV DQYREQLIAR VTSVEVVLDK LHGQVLSQEQ YERVLAENTR PSQMRKLFSL SQSWDRKCKD GLYQALKET HPHLIMELWE KGSKK UniProtKB: NACHT, LRR and PYD domains-containing protein 1 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 8 |
---|---|
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / 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 |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 5-35 / Number real images: 2187 / Average electron dose: 80.0 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 / Nominal magnification: 115000 |
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 |
---|---|
Output model | PDB-6k7v: |