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- PDB-2kn6: Structure of full-length human ASC (Apoptosis-associated speck-li... -

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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 / The AIM2 inflammasome / AIM2 inflammasome complex / 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 / icosanoid biosynthetic process ...Pyrin domain binding / NLRP6 inflammasome complex / myosin I binding / The AIM2 inflammasome / AIM2 inflammasome complex / 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 / icosanoid biosynthetic process / IkappaB kinase complex / NLRP1 inflammasome complex / canonical inflammasome complex / macropinocytosis / interleukin-6 receptor binding / NLRP3 inflammasome complex / NLRP3 inflammasome complex assembly / BMP receptor binding / positive regulation of adaptive immune response / osmosensory signaling pathway / positive regulation of cysteine-type endopeptidase activity / pattern recognition receptor signaling pathway / negative regulation of protein serine/threonine kinase activity / negative regulation of interferon-beta production / CLEC7A/inflammasome pathway / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of macrophage cytokine production / positive regulation of actin filament polymerization / negative regulation of NF-kappaB transcription factor activity / tropomyosin binding / positive regulation of release of cytochrome c from mitochondria / pyroptotic inflammatory response / : / positive regulation of activated T cell proliferation / cysteine-type endopeptidase activator activity involved in apoptotic process / The NLRP3 inflammasome / positive regulation of interleukin-10 production / intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to interleukin-1 / 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 / Purinergic signaling in leishmaniasis infection / positive regulation of defense response to virus by host / negative regulation of canonical NF-kappaB signal transduction / positive regulation of phagocytosis / activation of innate immune response / positive regulation of chemokine production / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-1 beta production / regulation of autophagy / positive regulation of interleukin-8 production / positive regulation of JNK cascade / positive regulation of DNA-binding transcription factor activity / regulation of protein stability / protein homooligomerization / : / positive regulation of inflammatory response / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / SARS-CoV-1 activates/modulates innate immune responses / azurophil granule lumen / positive regulation of tumor necrosis factor 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 / protease binding / defense response to virus / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / transmembrane transporter binding / microtubule / 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 / Neutrophil degranulation / nucleolus / apoptotic process / 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 / : / Death Domain, Fas / Death Domain, Fas / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / CARD domain / CARD caspase recruitment domain profile. ...CARD8/ASC/NALP1, CARD domain / : / Death Domain, Fas / Death Domain, Fas / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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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

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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

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NMR measurement

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

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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

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