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- EMDB-30459: Cryo-EM map of rNLRP1-FIIND-CARD S969A mutant in complex with rDPP9 -

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Basic information

Entry
Database: EMDB / ID: EMD-30459
TitleCryo-EM map of rNLRP1-FIIND-CARD S969A mutant in complex with rDPP9
Map data
Sample
  • Complex: Complex of rNLRP1-FIIND S969A mutant with rDPP9 dimer
Function / homology
Function and homology information


negative regulation of cellular defense response / NLRP1 inflammasome complex assembly / cysteine-type endopeptidase activator activity / NLRP1 inflammasome complex / canonical inflammasome complex / programmed necrotic cell death / positive regulation of pyroptosis / self proteolysis / dipeptidyl-peptidase activity / Hydrolases; Acting on peptide bonds (peptidases) ...negative regulation of cellular defense response / NLRP1 inflammasome complex assembly / cysteine-type endopeptidase activator activity / NLRP1 inflammasome complex / canonical inflammasome complex / programmed necrotic cell death / positive regulation of pyroptosis / self proteolysis / dipeptidyl-peptidase activity / Hydrolases; Acting on peptide bonds (peptidases) / pattern recognition receptor activity / cellular response to UV-B / stress-activated protein kinase signaling cascade / pyroptosis / cell leading edge / antiviral innate immune response / response to muramyl dipeptide / signaling adaptor activity / molecular condensate scaffold activity / serine-type peptidase activity / positive regulation of interleukin-1 beta production / protein homooligomerization / positive regulation of inflammatory response / : / double-stranded RNA binding / peptidase activity / double-stranded DNA binding / scaffold protein binding / defense response to virus / neuron apoptotic process / regulation of apoptotic process / microtubule / defense response to bacterium / protein domain specific binding / neuronal cell body / enzyme binding / ATP hydrolysis activity / protein-containing complex / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
: / FIIND domain / Function to find / FIIND domain profile. / CARD8/ASC/NALP1, CARD domain / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / Leucine rich repeat, ribonuclease inhibitor type ...: / FIIND domain / Function to find / FIIND domain profile. / CARD8/ASC/NALP1, CARD domain / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / Leucine rich repeat, ribonuclease inhibitor type / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Leucine Rich repeat / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Death-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha/Beta hydrolase fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NACHT, LRR and PYD domains-containing protein 1 allele 2 / Dipeptidyl peptidase 9
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.69 Å
AuthorsHuang MH / Zhang XX / Chai JJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31421001 to J.C. China
CitationJournal: Nature / Year: 2021
Title: Structural and biochemical mechanisms of NLRP1 inhibition by DPP9.
Authors: Menghang Huang / Xiaoxiao Zhang / Gee Ann Toh / Qin Gong / Jia Wang / Zhifu Han / Bin Wu / Franklin Zhong / Jijie Chai /
Abstract: Nucleotide-binding domain, leucine-rich repeat receptors (NLRs) mediate innate immunity by forming inflammasomes. Activation of the NLR protein NLRP1 requires autocleavage within its function-to-find ...Nucleotide-binding domain, leucine-rich repeat receptors (NLRs) mediate innate immunity by forming inflammasomes. Activation of the NLR protein NLRP1 requires autocleavage within its function-to-find domain (FIIND). In resting cells, the dipeptidyl peptidases DPP8 and DPP9 interact with the FIIND of NLRP1 and suppress spontaneous NLRP1 activation; however, the mechanisms through which this occurs remain unknown. Here we present structural and biochemical evidence that full-length rat NLRP1 (rNLRP1) and rat DPP9 (rDPP9) form a 2:1 complex that contains an autoinhibited rNLRP1 molecule and an active UPA-CARD fragment of rNLRP1. The ZU5 domain is required not only for autoinhibition of rNLRP1 but also for assembly of the 2:1 complex. Formation of the complex prevents UPA-mediated higher-order oligomerization of UPA-CARD fragments and strengthens ZU5-mediated NLRP1 autoinhibition. Structure-guided biochemical and functional assays show that both NLRP1 binding and enzymatic activity are required for DPP9 to suppress NLRP1 in human cells. Together, our data reveal the mechanism of DPP9-mediated inhibition of NLRP1 and shed light on the activation of the NLRP1 inflammasome.
History
DepositionAug 14, 2020-
Header (metadata) releaseMar 31, 2021-
Map releaseMar 31, 2021-
UpdateMay 26, 2021-
Current statusMay 26, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30459.png

Downloads & links

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Map

FileDownload / File: emd_30459.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.091 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.028502792 - 0.06364959
Average (Standard dev.)0.00020999454 (±0.0018685114)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 261.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z261.840261.840261.840
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0290.0640.000

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Supplemental data

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Sample components

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Entire : Complex of rNLRP1-FIIND S969A mutant with rDPP9 dimer

EntireName: Complex of rNLRP1-FIIND S969A mutant with rDPP9 dimer
Components
  • Complex: Complex of rNLRP1-FIIND S969A mutant with rDPP9 dimer

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Supramolecule #1: Complex of rNLRP1-FIIND S969A mutant with rDPP9 dimer

SupramoleculeName: Complex of rNLRP1-FIIND S969A mutant with rDPP9 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 49.969 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 252425

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