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- EMDB-32406: Cryo-EM structure of bovine NLRP9 -

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Basic information

Entry
Database: EMDB / ID: EMD-32406
TitleCryo-EM structure of bovine NLRP9
Map data
Sample
  • Complex: NLRP9
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 9
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsNLR / 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
NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. ...NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / PAAD/DAPIN/Pyrin domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Death-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NACHT, LRR and PYD domains-containing protein 9
Similarity search - Component
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsKamitsukasa Y / Shimizu T
Funding support Japan, 2 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)19H03164 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)19H00976 Japan
CitationJournal: 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
DepositionDec 17, 2021-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32406.png

Downloads & links

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Map

FileDownload / File: emd_32406.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.245 Å
Density
Contour LevelBy AUTHOR: 5.13
Minimum - Maximum-22.164429999999999 - 28.695243999999999
Average (Standard dev.)0.000000000017837 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 174.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : NLRP9

EntireName: NLRP9
Components
  • Complex: NLRP9
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 9
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: NLRP9

SupramoleculeName: NLRP9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (cattle)

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Macromolecule #1: NACHT, LRR and PYD domains-containing protein 9

MacromoleculeName: NACHT, LRR and PYD domains-containing protein 9 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 106.627039 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Details: 10 mM Tris pH 8.0, 150 mM NaCl, 1 mM TCEP, 2 mM ADP
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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