[English] 日本語
Yorodumi
- PDB-2kn6: Structure of full-length human ASC (Apoptosis-associated speck-li... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kn6
TitleStructure of full-length human ASC (Apoptosis-associated speck-like protein containing a CARD)
ComponentsApoptosis-associated speck-like protein containing a CARD
KeywordsAPOPTOSIS / Multidomain modular protein structure / Interdomain mobility / Death domain / Inflammation
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 / regulation of intrinsic apoptotic signaling pathway / myeloid dendritic cell activation / IkappaB kinase complex / The AIM2 inflammasome / macropinocytosis ...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 / regulation of intrinsic apoptotic signaling pathway / myeloid dendritic cell activation / IkappaB kinase complex / The AIM2 inflammasome / macropinocytosis / AIM2 inflammasome complex / icosanoid biosynthetic process / interleukin-6 receptor binding / NLRP1 inflammasome complex / canonical inflammasome complex / NLRP3 inflammasome complex assembly / positive regulation of adaptive immune response / BMP receptor binding / NLRP3 inflammasome complex / negative regulation of protein serine/threonine kinase activity / negative regulation of interferon-beta production / CLEC7A/inflammasome pathway / positive regulation of cysteine-type endopeptidase activity / regulation of tumor necrosis factor-mediated signaling pathway / osmosensory signaling pathway / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of macrophage cytokine production / pattern recognition receptor signaling pathway / positive regulation of actin filament polymerization / negative regulation of NF-kappaB transcription factor activity / tropomyosin binding / positive regulation of activated T cell proliferation / pyroptotic inflammatory response / cysteine-type endopeptidase activator activity involved in apoptotic process / 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 / The NLRP3 inflammasome / 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 / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / negative regulation of canonical NF-kappaB signal transduction / positive regulation of phagocytosis / positive regulation of defense response to virus by host / tumor necrosis factor-mediated signaling pathway / activation of innate immune response / positive regulation of interleukin-1 beta production / regulation of autophagy / positive regulation of interleukin-8 production / positive regulation of JNK cascade / regulation of protein stability / protein homooligomerization / positive regulation of DNA-binding transcription factor activity / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / activation of cysteine-type endopeptidase activity involved in apoptotic process / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / azurophil granule lumen / positive regulation of type II interferon production / positive regulation of T cell activation / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide / secretory granule lumen / defense response to Gram-negative bacterium / microtubule / defense response to virus / protease binding / transmembrane transporter binding / positive regulation of ERK1 and ERK2 cascade / protein dimerization activity / defense response to Gram-positive bacterium / positive regulation of apoptotic process / 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 / cytoplasm / cytosol
Similarity search - Function
CARD8/ASC/NALP1, CARD domain / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / Death Domain, Fas / PAAD/DAPIN/Pyrin domain / Death Domain, Fas / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain ...CARD8/ASC/NALP1, CARD domain / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / Death Domain, Fas / PAAD/DAPIN/Pyrin domain / Death Domain, Fas / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Apoptosis-associated speck-like protein containing a CARD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsDe Alba, E.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Structure and interdomain dynamics of apoptosis-associated speck-like protein containing a CARD (ASC)
Authors: de Alba, E.
#1: Journal: Biomol.Nmr Assign. / Year: 2007
Title: 1H, 15N and 13C backbone and side chain chemical shifts of human ASC (apoptosis-associated speck-like protein containing a CARD domain)
Authors: de Alba, E.
History
DepositionAug 16, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Apoptosis-associated speck-like protein containing a CARD


Theoretical massNumber of molelcules
Total (without water)23,8231
Polymers23,8231
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

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


Mass: 23823.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASC, CARD5, PYCARD, TMS1 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYS / References: UniProt: Q9ULZ3

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1223D 1H-15N NOESY
1313D HBHA(CO)NH
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HNCO
1713D H(CCO)NH
1813D C(CO)NH
1934D HCHC NOESY
NMR detailsText: Spectrometer with cryoprobe

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.2mM [U-100% 13C; U-100% 15N] Apoptosis-associated speck-like protein containing a CARD-1, 0.1mM sodium azide-2, 5mM [U-2H] TCEP-3, 95% H2O/5% D2O95% H2O/5% D2O
20.2mM [U-15N] Apoptosis-associated speck-like protein containing a CARD-4, 0.1mM sodium azide-5, 5mM TCEP-6, 95% H2O/5% D2O95% H2O/5% D2O
30.2mM [U-13C; U-15N] Apoptosis-associated speck-like protein containing a CARD-7, 0.1mM sodium azide-8, 5mM [U-2H] TCEP-9, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMApoptosis-associated speck-like protein containing a CARD-1[U-100% 13C; U-100% 15N]1
0.1 mMsodium azide-21
5 mMTCEP-3[U-2H]1
0.2 mMApoptosis-associated speck-like protein containing a CARD-4[U-15N]2
0.1 mMsodium azide-52
5 mMTCEP-62
0.2 mMApoptosis-associated speck-like protein containing a CARD-7[U-13C; U-15N]3
0.1 mMsodium azide-83
5 mMTCEP-9[U-2H]3
Sample conditionsIonic strength: 0 / pH: 3.8 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: BRUKER AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
XPLOR-NIHSchwieters, Kuszewski, Tjandra, Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxprocessing
XwinNMRBruker Biospincollection
PROCHECKNMRLaskowski, MacArthurdata analysis
TopSpinBruker Biospincollection
PIPPGarrettpeak picking
SparkyGoddarddata analysis
TALOSCornilescu, Delaglio, Baxgeometry optimization
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20 / Representative conformer: 1

+
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://pdbjlvh1.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