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- PDB-1ucp: NMR structure of the PYRIN domain of human ASC -

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Basic information

Entry
Database: PDB / ID: 1ucp
TitleNMR structure of the PYRIN domain of human ASC
ComponentsApoptosis-associated speck-like protein containing a CARD
KeywordsAPOPTOSIS / DEATH DOMAIN FOLD
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 / AIM2 inflammasome complex ...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 / AIM2 inflammasome complex / macropinocytosis / icosanoid biosynthetic process / NLRP1 inflammasome complex / interleukin-6 receptor binding / canonical inflammasome complex / NLRP3 inflammasome complex assembly / BMP receptor binding / NLRP3 inflammasome complex / positive regulation of adaptive immune response / osmosensory signaling pathway / 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 / 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 / positive regulation of actin filament polymerization / tropomyosin binding / pyroptotic inflammatory response / : / positive regulation of activated T cell proliferation / positive regulation of release of cytochrome c from mitochondria / cysteine-type endopeptidase activator activity involved in apoptotic process / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of interleukin-10 production / The NLRP3 inflammasome / 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 / negative regulation of canonical NF-kappaB signal transduction / positive regulation of phagocytosis / positive regulation of chemokine production / 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 / 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 / azurophil granule lumen / SARS-CoV-1 activates/modulates innate immune responses / 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 / secretory granule lumen / defense response to virus / defense response to Gram-negative bacterium / positive regulation of canonical NF-kappaB signal transduction / 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 / signal transduction / 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 / : / 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 / torsion angle dynamics
AuthorsLiepinsh, E. / Barbals, R. / Dahl, E. / Sharipo, A. / Staub, E. / Otting, G.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The death-domain fold of the ASC PYRIN domain, presenting a basis for PYRIN/PYRIN recognition
Authors: Liepinsh, E. / Barbals, R. / Dahl, E. / Sharipo, A. / Staub, E. / Otting, G.
History
DepositionApr 16, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)10,0921
Polymers10,0921
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 / 50structures with the least restraint violations,target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Apoptosis-associated speck-like protein containing a CARD / PYCARD / ASC


Mass: 10091.665 Da / Num. of mol.: 1 / Fragment: PYRIN DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: lymphocytes / Gene: ASC / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9ULZ3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131w1-decoupled NOESY
142DQF-COSY
1522D NOESY
1622D TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM PYRIN domain90% H2O/10% D2O
21mM PYRIN domain100% D2O
Sample conditionsIonic strength: 50mM / pH: 3.7 / Pressure: ambient / Temperature: 301 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentertstructure solution
OPAL2.6refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: 1118 NOE-derived distance restraints, 206 coupling constants
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,target function
Conformers calculated total number: 50 / Conformers submitted total number: 20

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