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- PDB-6n1h: Cryo-EM structure of ASC-CARD filament -

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Entry
Database: PDB / ID: 6n1h
TitleCryo-EM structure of ASC-CARD filament
ComponentsApoptosis-associated speck-like protein containing a CARD
KeywordsSIGNALING PROTEIN / Inflammasome / filament / immunity
Function / homologyDAPIN domain / The NLRP3 inflammasome / Death-like domain superfamily / CARD8/ASC/NALP1, CARD domain / Caspase recruitment domain / PAAD/DAPIN/Pyrin domain / CARD caspase recruitment domain profile. / DAPIN domain profile. / CLEC7A/inflammasome pathway / Neutrophil degranulation ...DAPIN domain / The NLRP3 inflammasome / Death-like domain superfamily / CARD8/ASC/NALP1, CARD domain / Caspase recruitment domain / PAAD/DAPIN/Pyrin domain / CARD caspase recruitment domain profile. / DAPIN domain profile. / CLEC7A/inflammasome pathway / Neutrophil degranulation / The AIM2 inflammasome / Peptidase C14 family / CARD domain / Pyrin domain binding / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / myosin I binding / myeloid dendritic cell activation involved in immune response / regulation of intrinsic apoptotic signaling pathway / myeloid dendritic cell activation / IkappaB kinase complex / BMP receptor binding / negative regulation of interferon-beta production / NLRP1 inflammasome complex / macropinocytosis / NLRP3 inflammasome complex / AIM2 inflammasome complex / interleukin-6 receptor binding / positive regulation of interleukin-10 secretion / positive regulation of adaptive immune response / interleukin-1 beta production / positive regulation of interleukin-8 secretion / positive regulation of chemokine secretion / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of T cell activation / negative regulation of protein serine/threonine kinase activity / activation of cysteine-type endopeptidase activity / positive regulation of cysteine-type endopeptidase activity / positive regulation of interleukin-1 beta secretion / activation of innate immune response / tropomyosin binding / positive regulation of activated T cell proliferation / positive regulation of defense response to virus by host / positive regulation of interleukin-6 secretion / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of T cell migration / regulation of tumor necrosis factor-mediated signaling pathway / cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of phagocytosis / positive regulation of actin filament polymerization / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of NF-kappaB transcription factor activity / positive regulation of release of cytochrome c from mitochondria / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-6 production / regulation of GTPase activity / regulation of autophagy / negative regulation of cytokine production involved in inflammatory response / cellular response to interleukin-1 / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of tumor necrosis factor production / negative regulation of I-kappaB kinase/NF-kappaB signaling / positive regulation of JNK cascade / positive regulation of interferon-gamma production / regulation of protein stability / activation of cysteine-type endopeptidase activity involved in apoptotic process / azurophil granule lumen / intrinsic apoptotic signaling pathway in response to DNA damage / defense response to virus / cellular response to tumor necrosis factor / ion channel binding / positive regulation of DNA-binding transcription factor activity / protein homooligomerization / secretory granule lumen / positive regulation of ERK1 and ERK2 cascade / protease binding / positive regulation of NF-kappaB transcription factor activity / protein dimerization activity / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / inflammatory response / positive regulation of apoptotic process / apoptotic process / neuronal cell body / nucleolus / innate immune response / neutrophil degranulation / endoplasmic reticulum / signal transduction / enzyme binding / mitochondrion / protein homodimerization activity / extracellular region / identical protein binding / nucleus / cytosol / cytoplasm / Apoptosis-associated speck-like protein containing a CARD
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.17 Å resolution
AuthorsLi, Y. / Fu, T. / Wu, H.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Cryo-EM structures of ASC and NLRC4 CARD filaments reveal a unified mechanism of nucleation and activation of caspase-1.
Authors: Yang Li / Tian-Min Fu / Alvin Lu / Kristen Witt / Jianbin Ruan / Chen Shen / Hao Wu
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 8, 2018 / Release: Dec 5, 2018

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Assembly

Deposited unit
A: Apoptosis-associated speck-like protein containing a CARD
B: Apoptosis-associated speck-like protein containing a CARD
C: Apoptosis-associated speck-like protein containing a CARD
D: Apoptosis-associated speck-like protein containing a CARD
E: Apoptosis-associated speck-like protein containing a CARD
F: Apoptosis-associated speck-like protein containing a CARD
G: Apoptosis-associated speck-like protein containing a CARD
H: Apoptosis-associated speck-like protein containing a CARD
I: Apoptosis-associated speck-like protein containing a CARD
J: Apoptosis-associated speck-like protein containing a CARD
K: Apoptosis-associated speck-like protein containing a CARD
L: Apoptosis-associated speck-like protein containing a CARD
M: Apoptosis-associated speck-like protein containing a CARD
N: Apoptosis-associated speck-like protein containing a CARD
O: Apoptosis-associated speck-like protein containing a CARD
P: Apoptosis-associated speck-like protein containing a CARD


Theoretical massNumber of molelcules
Total (without water)156,40216
Polyers156,40216
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)27310
ΔGint (kcal/M)-50
Surface area (Å2)52500
Helical symmetryCircular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 16 / Rise per n subunits: 5 Å / Rotation per n subunits: -100.58 deg.

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Components

#1: Protein/peptide
Apoptosis-associated speck-like protein containing a CARD / hASC / Caspase recruitment domain-containing protein 5 / PYD and CARD domain-containing protein / Target of methylation-induced silencing 1


Mass: 9775.143 Da / Num. of mol.: 16 / Fragment: CARD (UNP residues 112-194) / Source: (gene. exp.) Homo sapiens (human) / Gene: PYCARD, ASC, CARD5, TMS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ULZ3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: ASC-CARD filament / Type: CELL / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 41 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -100.58 deg. / Axial rise/subunit: 5 Å / Axial symmetry: C1
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 226603 / Symmetry type: HELICAL

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