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- EMDB-9947: Structure of ASC CARD filament -

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Basic information

Entry
Database: EMDB / ID: EMD-9947
TitleStructure of ASC CARD filament
Map dataNone
Sample
  • Complex: ASC CARD filament
    • Protein or peptide: Apoptosis-associated speck-like protein containing a CARD
Keywordsfilament / SIGNALING PROTEIN
Function / homology
Function and homology information


Pyrin domain binding / NLRP6 inflammasome complex / myosin I binding / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / myeloid dendritic cell activation involved in immune response / negative regulation of protein serine/threonine kinase activity / regulation of intrinsic apoptotic signaling pathway / myeloid dendritic cell activation / IkappaB kinase complex / The AIM2 inflammasome ...Pyrin domain binding / NLRP6 inflammasome complex / myosin I binding / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / myeloid dendritic cell activation involved in immune response / negative regulation of protein serine/threonine kinase activity / regulation of intrinsic apoptotic signaling pathway / myeloid dendritic cell activation / IkappaB kinase complex / The AIM2 inflammasome / AIM2 inflammasome complex / icosanoid biosynthetic process / macropinocytosis / NLRP1 inflammasome complex / canonical inflammasome complex / interleukin-6 receptor binding / NLRP3 inflammasome complex assembly / BMP receptor binding / positive regulation of adaptive immune response / NLRP3 inflammasome complex / cysteine-type endopeptidase activator activity / CLEC7A/inflammasome pathway / osmosensory signaling pathway / negative regulation of interferon-beta production / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of extrinsic apoptotic signaling pathway / pattern recognition receptor signaling pathway / positive regulation of macrophage cytokine production / negative regulation of NF-kappaB transcription factor activity / pattern recognition receptor activity / tropomyosin binding / pyroptotic inflammatory response / positive regulation of actin filament polymerization / positive regulation of release of cytochrome c from mitochondria / positive regulation of activated T cell proliferation / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of interleukin-10 production / The NLRP3 inflammasome / cellular response to interleukin-1 / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of T cell migration / positive regulation of DNA-binding transcription factor activity / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / positive regulation of defense response to virus by host / negative regulation of canonical NF-kappaB signal transduction / negative regulation of cytokine production involved in inflammatory response / activation of innate immune response / intrinsic apoptotic signaling pathway / positive regulation of phagocytosis / positive regulation of interleukin-1 beta production / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-8 production / positive regulation of JNK cascade / apoptotic signaling pathway / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / protein homooligomerization / positive regulation of T cell activation / regulation of protein stability / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of type II interferon production / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / azurophil granule lumen / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / regulation of inflammatory response / protease binding / secretory granule lumen / defense response to Gram-negative bacterium / defense response to virus / microtubule / transmembrane transporter binding / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / protein dimerization activity / defense response to Gram-positive bacterium / regulation of autophagy / positive regulation of apoptotic process / inflammatory response / Golgi membrane / innate immune response / neuronal cell body / apoptotic process / Neutrophil degranulation / nucleolus / enzyme binding / endoplasmic reticulum / signal transduction / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
CARD8/ASC/NALP1, CARD domain / : / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily
Similarity search - Domain/homology
Apoptosis-associated speck-like protein containing a CARD
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsGong Q / Xu C
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: Gong Q / Robinson K / Xu C / Huynh PT / Chong KHC / Tan EYJ / Zhang J / Boo ZZ / Teo DET / Lay K / Zhang Y / Lim JSY / Goh WI / Wright G / Zhong FL / Reversade B / Wu B
History
DepositionJun 14, 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: 0.0135
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0135
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6k99
  • Surface level: 0.0135
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6k99
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_9947.map.gz / Format: CCP4 / Size: 4.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.0135 / Movie #1: 0.0135
Minimum - Maximum-0.007267787 - 0.023820158
Average (Standard dev.)0.0014931795 (±0.0038332199)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin394857
Dimensions11711398
Spacing11311798
CellA: 124.3 Å / B: 128.7 Å / C: 107.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z11311798
origin x/y/z0.0000.0000.000
length x/y/z124.300128.700107.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS483957
NC/NR/NS11311798
D min/max/mean-0.0070.0240.001

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Supplemental data

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Sample components

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Entire : ASC CARD filament

EntireName: ASC CARD filament
Components
  • Complex: ASC CARD filament
    • Protein or peptide: Apoptosis-associated speck-like protein containing a CARD

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Supramolecule #1: ASC CARD filament

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

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Macromolecule #1: Apoptosis-associated speck-like protein containing a CARD

MacromoleculeName: Apoptosis-associated speck-like protein containing a CARD
type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.775143 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
LHFIDQHRAA LIARVTNVEW LLDALYGKVL TDEQYQAVRA EPTNPSKMRK LFSFTPAWNW TCKDLLLQAL RESQSYLVED LER

UniProtKB: Apoptosis-associated speck-like protein containing a CARD

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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 R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 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) / Number real images: 3183 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.5 µm / Calibrated defocus min: 1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / 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: 5.27 Å
Applied symmetry - Helical parameters - Δ&Phi: -100.614 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 59566
Segment selectionNumber selected: 877408 / Software - Name: RELION (ver. 2.0)
Startup modelType of model: OTHER / Details: solid column
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.0)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6k99:
Structure of ASC CARD filament

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