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- EMDB-9943: Structure of NLRP1 CARD filament -

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Basic information

Entry
Database: EMDB / ID: EMD-9943
TitleStructure of NLRP1 CARD filament
Map dataNone
Sample
  • Complex: NLRP1 CARD filament
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 1
Keywordsfilament / SIGNALING PROTEIN
Function / homology
Function and homology information


NLRP1 inflammasome complex assembly / NLRP1 inflammasome complex / The NLRP1 inflammasome / NLRP3 inflammasome complex / self proteolysis / cysteine-type endopeptidase activator activity / Hydrolases; Acting on peptide bonds (peptidases) / pattern recognition receptor signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process / cellular response to UV-B ...NLRP1 inflammasome complex assembly / NLRP1 inflammasome complex / The NLRP1 inflammasome / NLRP3 inflammasome complex / self proteolysis / cysteine-type endopeptidase activator activity / Hydrolases; Acting on peptide bonds (peptidases) / pattern recognition receptor signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process / cellular response to UV-B / pattern recognition receptor activity / pyroptotic inflammatory response / response to muramyl dipeptide / signaling adaptor activity / antiviral innate immune response / intrinsic apoptotic signaling pathway / activation of innate immune response / positive regulation of interleukin-1 beta production / molecular condensate scaffold activity / protein homooligomerization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / positive regulation of inflammatory response / peptidase activity / double-stranded RNA binding / regulation of inflammatory response / double-stranded DNA binding / neuron apoptotic process / regulation of apoptotic process / defense response to virus / defense response to bacterium / inflammatory response / protein domain specific binding / apoptotic process / nucleolus / enzyme binding / signal transduction / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
FIIND domain / Function to find / UPA-FIIND domain / 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 ...FIIND domain / Function to find / UPA-FIIND domain / 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 / DAPIN domain / NACHT nucleoside triphosphatase / NACHT domain / DAPIN domain profile. / NACHT-NTPase domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Leucine rich repeat, ribonuclease inhibitor type / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Leucine Rich repeat / Leucine Rich Repeat / Death-like domain superfamily / Leucine-rich repeat profile. / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsQin G / Chenrui X
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (Singapore)tier2 and tier1 Singapore
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for distinct inflammasome complex assembly by human NLRP1 and CARD8.
Authors: Qin Gong / Kim Robinson / Chenrui Xu / Phuong Thao Huynh / Kelvin Han Chung Chong / Eddie Yong Jun Tan / Jiawen Zhang / Zhao Zhi Boo / Daniel Eng Thiam Teo / Kenneth Lay / Yaming Zhang / ...Authors: Qin Gong / Kim Robinson / Chenrui Xu / Phuong Thao Huynh / Kelvin Han Chung Chong / Eddie Yong Jun Tan / Jiawen Zhang / Zhao Zhi Boo / Daniel Eng Thiam Teo / Kenneth Lay / Yaming Zhang / John Soon Yew Lim / Wah Ing Goh / Graham Wright / Franklin L Zhong / Bruno Reversade / Bin Wu /
Abstract: Nod-like receptor (NLR) proteins activate pyroptotic cell death and IL-1 driven inflammation by assembling and activating the inflammasome complex. Closely related sensor proteins NLRP1 and CARD8 ...Nod-like receptor (NLR) proteins activate pyroptotic cell death and IL-1 driven inflammation by assembling and activating the inflammasome complex. Closely related sensor proteins NLRP1 and CARD8 undergo unique auto-proteolysis-dependent activation and are implicated in auto-inflammatory diseases; however, their mechanisms of activation are not understood. Here we report the structural basis of how the activating domains (FIIND-CARD) of NLRP1 and CARD8 self-oligomerize to assemble distinct inflammasome complexes. Recombinant FIIND-CARD of NLRP1 forms a two-layered filament, with an inner core of oligomerized CARD surrounded by an outer ring of FIIND. Biochemically, self-assembled NLRP1-CARD filaments are sufficient to drive ASC speck formation in cultured human cells-a process that is greatly enhanced by NLRP1-FIIND which forms oligomers in vitro. The cryo-EM structures of NLRP1-CARD and CARD8-CARD filaments, solved here at 3.7 Å, uncover unique structural features that enable NLRP1 and CARD8 to discriminate between ASC and pro-caspase-1. In summary, our findings provide structural insight into the mechanisms of activation for human NLRP1 and CARD8 and reveal how highly specific signaling can be achieved by heterotypic CARD interactions within the inflammasome complexes.
History
DepositionJun 9, 2019-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0165
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0165
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6k7v
  • Surface level: 0.0165
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6k7v
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9943.png

Downloads & links

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Map

FileDownload / File: emd_9943.map.gz / Format: CCP4 / Size: 5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 109 pix.
= 119.9 Å		1.1 Å/pix.
x 109 pix.
= 119.9 Å		1.1 Å/pix.
x 110 pix.
= 121. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0165 / Movie #1: 0.0165
Minimum - Maximum-0.0028687578 - 0.028917545
Average (Standard dev.)0.003999996 (±0.0051597194)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin656164
Dimensions109110109
Spacing110109109
CellA: 121.0 Å / B: 119.9 Å / C: 119.9 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z110109109
origin x/y/z0.0000.0000.000
length x/y/z121.000119.900119.900
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS616564
NC/NR/NS110109109
D min/max/mean-0.0030.0290.004

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Supplemental data

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Additional map: cropped out 12mer density used in qseudo-crystallographic refinement,...

Fileemd_9943_additional.map
Annotationcropped out 12mer density used in qseudo-crystallographic refinement, not for publication.
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_9943_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_9943_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : NLRP1 CARD filament

EntireName: NLRP1 CARD filament
Components
  • Complex: NLRP1 CARD filament
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 1

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Supramolecule #1: NLRP1 CARD filament

SupramoleculeName: NLRP1 CARD filament / 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 1

MacromoleculeName: NACHT, LRR and PYD domains-containing protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.203776 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
GPGDYKDDDD KDAPQLLHFV DQYREQLIAR VTSVEVVLDK LHGQVLSQEQ YERVLAENTR PSQMRKLFSL SQSWDRKCKD GLYQALKET HPHLIMELWE KGSKK

UniProtKB: NACHT, LRR and PYD domains-containing protein 1

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 5-35 / Number real images: 2187 / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 115000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.36 Å
Applied symmetry - Helical parameters - Δ&Phi: -100.821 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 53241
Segment selectionNumber selected: 422388
Startup modelType of model: OTHER / Details: solid column
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6k7v:
Structure of NLRP1 CARD filament

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