+Open data
-Basic information
Entry | Database: PDB / ID: 7wbu | |||||||||
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Title | Cryo-EM structure of bovine NLRP9 | |||||||||
Components | NACHT, LRR and PYD domains-containing protein 9 | |||||||||
Keywords | IMMUNE SYSTEM / NLR / NOD-like receptor / NLRP9 / Inflammasome | |||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.42 Å | |||||||||
Authors | Kamitsukasa, Y. / Shimizu, T. / Ohto, U. | |||||||||
Funding support | Japan, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wbu.cif.gz | 230.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wbu.ent.gz | 171.8 KB | Display | PDB format |
PDBx/mmJSON format | 7wbu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wbu_validation.pdf.gz | 932.1 KB | Display | wwPDB validaton report |
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Full document | 7wbu_full_validation.pdf.gz | 941.3 KB | Display | |
Data in XML | 7wbu_validation.xml.gz | 29.4 KB | Display | |
Data in CIF | 7wbu_validation.cif.gz | 43.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/7wbu ftp://data.pdbj.org/pub/pdb/validation_reports/wb/7wbu | HTTPS FTP |
-Related structure data
Related structure data | 32406MC 7wbtC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 106627.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: NLRP9, NALP9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q288C4 |
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#2: Chemical | ChemComp-ADP / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: NLRP9 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Bos taurus (cattle) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 Details: 10 mM Tris pH 8.0, 150 mM NaCl, 1 mM TCEP, 2 mM ADP |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50000 / Symmetry type: POINT |