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(-) Description

Title :  SOLUTION STRUCTURE OF THE PYRIN DOMAIN OF HUMAN PYRIN
 
Authors :  S. L. Soh, S. J. Smith, J. M. Hill
Date :  15 May 14  (Deposition) - 16 Jul 14  (Release) - 16 Jul 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
NMR Structure *:  A  (1x)
Keywords :  Pyrin Domain, Death Domain, Inflammation, Cs-Rosetta, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. R. Vajjhala, S. Kaiser, S. J. Smith, Q. Ong, S. L. Soh, K. J. Stacey, J. M. Hill
Identification Of Multifaceted Binding Modes For Pyrin And Asc Pyrin Domains Gives Insights Into Pyrin Inflammasome Assembly
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PYRIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System VectorPET-28B
    Expression System Vector TypeVECTOR
    FragmentDAPIN DOMAIN (PYD), RESIDUES 1-92
    GeneMEFV, MEF
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMARENOSTRIN

 Structural Features

(-) Chains, Units

  1
NMR Structure (10x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2MPC)

(-) Sites  (0, 0)

(no "Site" information available for 2MPC)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2MPC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2MPC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

NMR Structure (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048398V33LMEFV_HUMANPolymorphism11466016AV33L
2UniProtVAR_028326R42WMEFV_HUMANDisease (ARFMF)61754767AR42W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
NMR Structure * (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048398V33LMEFV_HUMANPolymorphism11466016AV33L
2UniProtVAR_028326R42WMEFV_HUMANDisease (ARFMF)61754767AR42W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2MPC)

(-) Exons   (0, 0)

(no "Exon" information available for 2MPC)

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:90
 aligned with MEFV_HUMAN | O15553 from UniProtKB/Swiss-Prot  Length:781

    Alignment length:90
                                    13        23        33        43        53        63        73        83        93
            MEFV_HUMAN    4 TPSDHLLSTLEELVPYDFEKFKFKLQNTSVQKEHSRIPRSQIQRARPVKMATLLVTYYGEEYAVQLTLQVLRAINQRLLAEELHRAAIQE 93
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------L--------W--------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                  2mpc A  4 TPSDHLLSTLEELVPYDFEKFKFKLQNTSVQKEHSRIPRSQIQRARPVKMATLLVTYYGEEYAVQLTLQVLRAINQRLLAEELHRAAIQL 93
                                    13        23        33        43        53        63        73        83        93

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  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2MPC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2MPC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2MPC)

(-) Gene Ontology  (28, 28)

NMR Structure(hide GO term definitions)
Chain A   (MEFV_HUMAN | O15553)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:1900226    negative regulation of NLRP3 inflammasome complex assembly    Any process that stops, prevents or reduces the frequency, rate or extent of NLRP3 inflammasome complex assembly.
    GO:1900016    negative regulation of cytokine production involved in inflammatory response    Any process that stops, prevents or reduces the frequency, rate or extent of cytokine production involved in inflammatory response.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0032691    negative regulation of interleukin-1 beta production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-1 beta production.
    GO:0032695    negative regulation of interleukin-12 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-12 production.
    GO:0071641    negative regulation of macrophage inflammatory protein 1 alpha production    Any process that stops, prevents, or reduces the frequency, rate, or extent of production of macrophage inflammatory protein 1 alpha.
    GO:0010508    positive regulation of autophagy    Any process that activates, maintains or increases the rate of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:2001056    positive regulation of cysteine-type endopeptidase activity    Any process that activates or increases the frequency, rate or extent of cysteine-type endopeptidase activity.
    GO:0034341    response to interferon-gamma    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-gamma stimulus. Interferon-gamma is also known as type II interferon.
cellular component
    GO:0005776    autophagosome    A double-membrane-bounded compartment that engulfs endogenous cellular material as well as invading microorganisms to target them to the vacuole/lysosome for degradation as part of macroautophagy.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0005875    microtubule associated complex    Any multimeric complex connected to a microtubule.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MEFV_HUMAN | O155532wl1 4cg4

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