[English] 日本語
Yorodumi
- EMDB-2971: Structure and assembly of the mouse ASC filament -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2971
TitleStructure and assembly of the mouse ASC filament
Map dataReconstruction of ASC-PYD filament
Sample
  • Sample: Mouse ASC-PYD filament
  • Protein or peptide: mouse ASC filament
KeywordsASC Apoptosis associated speck like protein containing a CARD / CARD caspase recruitment and activation domain / PYD PYRIN domain / PYHIN pyrin domain and hematopoietic expression / interferon inducibility / nuclear localization domain containing / NLR NOD like receptor / BIR Baculovirus IAP repeat domain
Function / homology
Function and homology information


interleukin-1 beta production / CLEC7A/inflammasome pathway / positive regulation of chemokine production => GO:0032722 / Pyrin domain binding / myosin I binding / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / regulation of cysteine-type endopeptidase activity involved in apoptotic process / myeloid dendritic cell activation involved in immune response / regulation of intrinsic apoptotic signaling pathway / peptidase activator activity involved in apoptotic process ...interleukin-1 beta production / CLEC7A/inflammasome pathway / positive regulation of chemokine production => GO:0032722 / Pyrin domain binding / myosin I binding / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / regulation of cysteine-type endopeptidase activity involved in apoptotic process / myeloid dendritic cell activation involved in immune response / regulation of intrinsic apoptotic signaling pathway / peptidase activator activity involved in apoptotic process / myeloid dendritic cell activation / IkappaB kinase complex / AIM2 inflammasome complex / macropinocytosis / NLRP1 inflammasome complex / interleukin-6 receptor binding / positive regulation of adaptive immune response / NLRP3 inflammasome complex / BMP receptor binding / negative regulation of protein serine/threonine kinase activity / negative regulation of interferon-beta production / positive regulation of cysteine-type endopeptidase activity / regulation of tumor necrosis factor-mediated signaling pathway / activation of cysteine-type endopeptidase activity / positive regulation of extrinsic apoptotic signaling pathway / cysteine-type endopeptidase activity involved in apoptotic process / tropomyosin binding / positive regulation of actin filament polymerization / regulation of GTPase activity / negative regulation of NF-kappaB transcription factor activity / positive regulation of activated T cell proliferation / positive regulation of release of cytochrome c from mitochondria / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of interleukin-10 production / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of cytokine production involved in inflammatory response / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of T cell migration / cellular response to interleukin-1 / positive regulation of phagocytosis / negative regulation of canonical NF-kappaB signal transduction / positive regulation of defense response to virus by host / tumor necrosis factor-mediated signaling pathway / activation of innate immune response / Neutrophil degranulation / positive regulation of interleukin-1 beta production / regulation of autophagy / positive regulation of interleukin-8 production / response to bacterium / positive regulation of JNK cascade / regulation of protein stability / protein homooligomerization / positive regulation of interleukin-6 production / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of DNA-binding transcription factor activity / positive regulation of T cell activation / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / defense response to virus / regulation of apoptotic process / cellular response to lipopolysaccharide / protease binding / defense response to Gram-negative bacterium / transmembrane transporter binding / positive regulation of ERK1 and ERK2 cascade / protein dimerization activity / inflammatory response / positive regulation of apoptotic process / Golgi membrane / innate immune response / neuronal cell body / apoptotic process / nucleolus / enzyme binding / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
CARD8/ASC/NALP1, CARD domain / Peptidase C14 family / 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 speciesMus musculus (house mouse)
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsSborgi L / Ravotti F / Dandey VP / Dick MS / Mazur A / Reckel S / Chami M / Scherer S / Bockmann A / Egelman EH ...Sborgi L / Ravotti F / Dandey VP / Dick MS / Mazur A / Reckel S / Chami M / Scherer S / Bockmann A / Egelman EH / Stahlberg H / Broz P / Meier BH / Hiller S
CitationJournal: Proc Natl Acad Sci U S A / Year: 2015
Title: Structure and assembly of the mouse ASC inflammasome by combined NMR spectroscopy and cryo-electron microscopy.
Authors: Lorenzo Sborgi / Francesco Ravotti / Venkata P Dandey / Mathias S Dick / Adam Mazur / Sina Reckel / Mohamed Chami / Sebastian Scherer / Matthias Huber / Anja Böckmann / Edward H Egelman / ...Authors: Lorenzo Sborgi / Francesco Ravotti / Venkata P Dandey / Mathias S Dick / Adam Mazur / Sina Reckel / Mohamed Chami / Sebastian Scherer / Matthias Huber / Anja Böckmann / Edward H Egelman / Henning Stahlberg / Petr Broz / Beat H Meier / Sebastian Hiller /
Abstract: Inflammasomes are multiprotein complexes that control the innate immune response by activating caspase-1, thus promoting the secretion of cytokines in response to invading pathogens and endogenous ...Inflammasomes are multiprotein complexes that control the innate immune response by activating caspase-1, thus promoting the secretion of cytokines in response to invading pathogens and endogenous triggers. Assembly of inflammasomes is induced by activation of a receptor protein. Many inflammasome receptors require the adapter protein ASC [apoptosis-associated speck-like protein containing a caspase-recruitment domain (CARD)], which consists of two domains, the N-terminal pyrin domain (PYD) and the C-terminal CARD. Upon activation, ASC forms large oligomeric filaments, which facilitate procaspase-1 recruitment. Here, we characterize the structure and filament formation of mouse ASC in vitro at atomic resolution. Information from cryo-electron microscopy and solid-state NMR spectroscopy is combined in a single structure calculation to obtain the atomic-resolution structure of the ASC filament. Perturbations of NMR resonances upon filament formation monitor the specific binding interfaces of ASC-PYD association. Importantly, NMR experiments show the rigidity of the PYD forming the core of the filament as well as the high mobility of the CARD relative to this core. The findings are validated by structure-based mutagenesis experiments in cultured macrophages. The 3D structure of the mouse ASC-PYD filament is highly similar to the recently determined human ASC-PYD filament, suggesting evolutionary conservation of ASC-dependent inflammasome mechanisms.
History
DepositionMar 31, 2015-
Header (metadata) releaseMay 6, 2015-
Map releaseOct 14, 2015-
UpdateNov 25, 2015-
Current statusNov 25, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 25
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 25
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2n1f
  • Surface level: 25
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2n1f
  • Surface level: 25
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2n1f
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2971.jpg

Downloads & links

-
Map

FileDownload / File: emd_2971.map.gz / Format: CCP4 / Size: 23.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of ASC-PYD filament
Voxel sizeX=Y=Z: 0.67 Å
Density
Contour LevelBy EMDB: 20.0 / Movie #1: 25
Minimum - Maximum-47.816951750000001 - 81.899246219999995
Average (Standard dev.)-2.8232131 (±11.493054389999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-79
Dimensions200200160
Spacing200200160
CellA: 134.0 Å / B: 134.0 Å / C: 107.200005 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.670.670.67
M x/y/z200200160
origin x/y/z0.0000.0000.000
length x/y/z134.000134.000107.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-100-100-79
NC/NR/NS200200160
D min/max/mean-47.81781.899-2.823

-
Supplemental data

-
Sample components

-
Entire : Mouse ASC-PYD filament

EntireName: Mouse ASC-PYD filament
Components
  • Sample: Mouse ASC-PYD filament
  • Protein or peptide: mouse ASC filament

-
Supramolecule #1000: Mouse ASC-PYD filament

SupramoleculeName: Mouse ASC-PYD filament / type: sample / ID: 1000 / Number unique components: 1

-
Macromolecule #1: mouse ASC filament

MacromoleculeName: mouse ASC filament / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: mouse
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: pLysS / Recombinant plasmid: pET28a

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 8 / Details: 25mM Tris 300mM NaCl
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
Details: vitrified by plunging into liquid nitrogen-cooled liquid ethane
Method: The grids were blotted for 1 s before plunging

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt angle min: -12 / Tilt angle max: 12
DateOct 10, 2014
Image recordingCategory: CCD / Film or detector model: DIRECT ELECTRON DE-10 (5k x 4k) / Digitization - Sampling interval: 5 µm / Number real images: 21138 / Average electron dose: 20 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: CTFFIND3
Final reconstructionApplied symmetry - Helical parameters - Δz: 14.2 Å
Applied symmetry - Helical parameters - Δ&Phi: 53 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: OTHER / Software - Name: EMAN2, IHRSR, SPIDER
DetailsThe particles were aligned using IHRSR

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more