+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32406 | |||||||||
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Title | Cryo-EM structure of bovine NLRP9 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | NLR / NOD-like receptor / NLRP9 / Inflammasome / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information canonical inflammasome complex / regulation of inflammatory response / inflammatory response / innate immune response / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.42 Å | |||||||||
Authors | Kamitsukasa Y / Shimizu T | |||||||||
Funding support | Japan, 2 items
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Citation | Journal: FEBS Lett / Year: 2022 Title: The structure of NLRP9 reveals a unique C-terminal region with putative regulatory function. Authors: Yukie Kamitsukasa / Kenji Nakano / Karin Murakami / Kunio Hirata / Masaki Yamamoto / Toshiyuki Shimizu / Umeharu Ohto / Abstract: Nucleotide-binding and oligomerisation domain-like receptors (NLRs) can form inflammasomes that activate caspase-1 and pro-interleukin-1β and induce pyroptosis. NLR family pyrin domain-containing 9 ...Nucleotide-binding and oligomerisation domain-like receptors (NLRs) can form inflammasomes that activate caspase-1 and pro-interleukin-1β and induce pyroptosis. NLR family pyrin domain-containing 9 (NLRP9) forms an inflammasome and activates innate immune responses during virus infection, but little is known about this process. Here, we report the crystal and cryo-electron microscopy structures of NLRP9 in an ADP-bound state, revealing inactive and closed conformations of NLRP9 and its similarities to other structurally characterised NLRs. Moreover, we found a C-terminal region interacting with the concave surface of the leucine-rich repeat domain of NLRP9. This region is unique among NLRs and might be involved in the specific function of NLRP9. These data provide the structural basis for understanding the mechanism of NLRP9 regulation and activation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32406.map.gz | 9.7 MB | EMDB map data format | |
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Header (meta data) | emd-32406-v30.xml emd-32406.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
Images | emd_32406.png | 104.2 KB | ||
Filedesc metadata | emd-32406.cif.gz | 5.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32406 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32406 | HTTPS FTP |
-Validation report
Summary document | emd_32406_validation.pdf.gz | 505.6 KB | Display | EMDB validaton report |
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Full document | emd_32406_full_validation.pdf.gz | 505.1 KB | Display | |
Data in XML | emd_32406_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | emd_32406_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32406 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32406 | HTTPS FTP |
-Related structure data
Related structure data | 7wbuMC 7wbtC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32406.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.245 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : NLRP9
Entire | Name: NLRP9 |
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Components |
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-Supramolecule #1: NLRP9
Supramolecule | Name: NLRP9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Bos taurus (cattle) |
-Macromolecule #1: NACHT, LRR and PYD domains-containing protein 9
Macromolecule | Name: NACHT, LRR and PYD domains-containing protein 9 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 106.627039 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: HHHHHHDYKD DDDKLEVLFQ GPEFRNEIRQ KINPYRSHMK QKFQVLWEKE PCLLVPEDFY EETTKIEYEL LSTVYLDAFK PGESSPTVV LHGPEGIGKT TFLRKVMLEW AKGNLWRDRF SFVFFLTGRE MNGVTDMSLV ELLSRDWPES SEPIEDIFSQ P ERILFILD ...String: HHHHHHDYKD DDDKLEVLFQ GPEFRNEIRQ KINPYRSHMK QKFQVLWEKE PCLLVPEDFY EETTKIEYEL LSTVYLDAFK PGESSPTVV LHGPEGIGKT TFLRKVMLEW AKGNLWRDRF SFVFFLTGRE MNGVTDMSLV ELLSRDWPES SEPIEDIFSQ P ERILFILD GMEELKFDLD CNADLCEDWE QPQSMQVVLQ SLLQKQMLPE CSLLLALSKM GMRKNYSLLK HMKCIFLLGF SE HQRKLYF SHYFQEKDAS SRAFSFVREK SSLFVLCQSP FLCWLVCTSL KCQLEKGEDL ELDSETITGL YVSFFTKVFR SGS ETCPLK QRRARLKSLC TLAAEGMWTC TFLFCPEDLR RNGVSESDTS MWLDMKLLHR SGDCLAFIHT CIQEFCAAMF YMFT RPKDP PHSVIGNVTQ LITRAVSGHY SRLSWTAVFL FVFSTERMTH RLETSFGFPL SKEIKQEITQ SLDTLSQCDP NNVMM SFQA LFNCLFETQD PEFVAQVVNF FKDIDIYIGT KEELIICAAC LRHCHSLQKF HLCMEHVFPD ESGCISNTIE KLTLWR DVC SAFAASEDFE ILNLDNCRFD EPSLAVLCRT LSQPVCKLRK FVCNFASNLA NSLELFKVIL HNPHLKHLNF YGSSLSH MD ARQLCEALKH PMCNIEELML GKCDITGEAC EDIASVLVHN KKLNLLSLCE NALKDDGVLV LCEALKNPDC ALEALLLS H CCFSSAACDH LSQVLLYNRS LTFLDLGSNV LKDEGVTTLC ESLKHPSCNL QELWLMNCYF TSVCCVDIAT VLIHSEKLK TLKLGNNKIY DAGAKQLCKA LKHPKCKLEN LGLEACELSP ASCEDLASAL TTCKSLTCVN LEWITLDYDG AAVLCEALVS LECSLQLLG LNKSSYDEEI KMMLTQVEEM NPNLIISHHL WTDDEGRRRG ILV UniProtKB: NACHT, LRR and PYD domains-containing protein 9 |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: 10 mM Tris pH 8.0, 150 mM NaCl, 1 mM TCEP, 2 mM ADP |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50000 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |