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- EMDB-0438: Cryo-EM structure of NLRP6 PYD filament -

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Basic information

Entry
Database: EMDB / ID: EMD-0438
TitleCryo-EM structure of NLRP6 PYD filament
Map dataNLRP6 PYD filament
Sample
  • Complex: NLRP6 PYD
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 6
Keywordsdeath domain fold / helical assembly / inflammasome / SIGNALING PROTEIN / PROTEIN FIBRIL
Function / homology
Function and homology information


regulation of mucus secretion / NLRP6 inflammasome complex assembly / neutrophil-mediated killing of gram-positive bacterium / positive regulation of interleukin-18-mediated signaling pathway / NLRP6 inflammasome complex / lipoteichoic acid binding / host-mediated regulation of intestinal microbiota composition / membraneless organelle / vasopressin receptor activity / acute inflammatory response to antigenic stimulus ...regulation of mucus secretion / NLRP6 inflammasome complex assembly / neutrophil-mediated killing of gram-positive bacterium / positive regulation of interleukin-18-mediated signaling pathway / NLRP6 inflammasome complex / lipoteichoic acid binding / host-mediated regulation of intestinal microbiota composition / membraneless organelle / vasopressin receptor activity / acute inflammatory response to antigenic stimulus / canonical inflammasome complex / acute inflammatory response / negative regulation of toll-like receptor signaling pathway / pattern recognition receptor activity / pyroptotic inflammatory response / necroptotic process / negative regulation of type II interferon production / negative regulation of canonical NF-kappaB signal transduction / signaling adaptor activity / antiviral innate immune response / regulation of autophagy / negative regulation of inflammatory response to antigenic stimulus / lipopolysaccharide binding / response to bacterium / peptide binding / molecular condensate scaffold activity / wound healing / protein homooligomerization / negative regulation of ERK1 and ERK2 cascade / positive regulation of inflammatory response / double-stranded RNA binding / regulation of inflammatory response / nuclear membrane / defense response to virus / defense response to Gram-positive bacterium / ATP binding / plasma membrane / cytosol / 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 / PAAD/DAPIN/Pyrin domain / NACHT nucleoside triphosphatase ...: / 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 / PAAD/DAPIN/Pyrin domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Leucine rich repeat, ribonuclease inhibitor type / Death-like domain superfamily / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NACHT, LRR and PYD domains-containing protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsShen C / Fu TM / Wu H
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Al124491 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)HD087988 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Molecular mechanism for NLRP6 inflammasome assembly and activation.
Authors: Chen Shen / Alvin Lu / Wen Jun Xie / Jianbin Ruan / Roberto Negro / Edward H Egelman / Tian-Min Fu / Hao Wu /
Abstract: Inflammasomes are large protein complexes that trigger host defense in cells by activating inflammatory caspases for cytokine maturation and pyroptosis. NLRP6 is a sensor protein in the nucleotide- ...Inflammasomes are large protein complexes that trigger host defense in cells by activating inflammatory caspases for cytokine maturation and pyroptosis. NLRP6 is a sensor protein in the nucleotide-binding domain (NBD) and leucine-rich repeat (LRR)-containing (NLR) inflammasome family that has been shown to play multiple roles in regulating inflammation and host defenses. Despite the significance of the NLRP6 inflammasome, little is known about the molecular mechanism behind its assembly and activation. Here we present cryo-EM and crystal structures of NLRP6 pyrin domain (PYD). We show that NLRP6 PYD alone is able to self-assemble into filamentous structures accompanied by large conformational changes and can recruit the ASC adaptor using PYD-PYD interactions. Using molecular dynamics simulations, we identify the surface that the NLRP6 PYD filament uses to recruit ASC PYD. We further find that full-length NLRP6 assembles in a concentration-dependent manner into wider filaments with a PYD core surrounded by the NBD and the LRR domain. These findings provide a structural understanding of inflammasome assembly by NLRP6 and other members of the NLR family.
History
DepositionDec 12, 2018-
Header (metadata) releaseJan 23, 2019-
Map releaseJan 23, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ncv
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ncv
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0438.png

Downloads & links

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Map

FileDownload / File: emd_0438.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNLRP6 PYD filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 180 pix.
= 190.8 Å		1.06 Å/pix.
x 180 pix.
= 190.8 Å		1.06 Å/pix.
x 180 pix.
= 190.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.15548103 - 0.32674178
Average (Standard dev.)0.0038273952 (±0.01951139)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 190.79999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z190.800190.800190.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.1550.3270.004

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Supplemental data

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Sample components

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Entire : NLRP6 PYD

EntireName: NLRP6 PYD
Components
  • Complex: NLRP6 PYD
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 6

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Supramolecule #1: NLRP6 PYD

SupramoleculeName: NLRP6 PYD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: NACHT, LRR and PYD domains-containing protein 6

MacromoleculeName: NACHT, LRR and PYD domains-containing protein 6 / type: protein_or_peptide / ID: 1 / Number of copies: 21 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.931579 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MDQPEAPCSS TGPRLAVARE LLLAALEELS QEQLKRFRHK LRDVGPDGRS IPWGRLERAD AVDLAEQLAQ FYGPEPALEV ARKTLKRAD ARDVAAQLQE RRLQRLG

UniProtKB: NACHT, LRR and PYD domains-containing protein 6

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 13.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 56.8 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 181477
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3j63

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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