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(-) Description

Title :  NMR STRUCTURE OF THE NALP1 PYRIN DOMAIN (PYD)
 
Authors :  S. Hiller, A. Kohl, F. Fiorito, T. Herrmann, G. Wider, J. Tschopp, M. G. Grutter, K. Wuthrich
Date :  12 Jun 03  (Deposition) - 07 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  5 Alpha-Helix Bundle, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Hiller, A. Kohl, F. Fiorito, T. Herrmann, G. Wider, J. Tschopp, M. G. Grutter, K. Wuthrich
Nmr Structure Of The Apoptosis- And Inflammation-Related Nalp1 Pyrin Domain
Structure V. 11 1199 2003
PubMed-ID: 14527388  |  Reference-DOI: 10.1016/J.STR.2003.08.009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NACHT-, LRR- AND PYD-CONTAINING PROTEIN 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET20B+
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentPYRIN DOMAIN (PYD)
    GeneNALP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsRESIDUES 1-56 CORRESPOND TO THE FUSED IMMUNOGLOBULIN G BINDING PROTEIN G (SWS P06654, RESIDUES 228-282)
    SynonymDEATH EFFECTOR FILAMENT-FORMING CED-4-LIKE APOPTOSIS PROTEIN, NUCLEOTIDE-BINDING DOMAIN AND CASPASE RECRUITMENT DOMAIN, CASPASE RECRUITMENT DOMAIN PROTEIN 7

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1PN5)

(-) Sites  (0, 0)

(no "Site" information available for 1PN5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PN5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PN5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069901M77TNLRP1_HUMANDisease (MSPC)397514692AM135T

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DAPINPS50824 DAPIN domain profile.NLRP1_HUMAN1-92  1A:59-150

(-) Exons   (0, 0)

(no "Exon" information available for 1PN5)

(-) 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
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:93
 aligned with NLRP1_HUMAN | Q9C000 from UniProtKB/Swiss-Prot  Length:1473

    Alignment length:93
                                    10        20        30        40        50        60        70        80        90   
          NLRP1_HUMAN     1 MAGGAWGRLACYLEFLKKEELKEFQLLLANKAHSRSSSGETPAQPEKTSGMEVASYLVAQYGEQRAWDLALHTWEQMGLRSLCAQAQEGAGHS  93
               SCOP domains d1pn5a1 A:59-151 NALP1                                                                        SCOP domains
               CATH domains 1pn5A00 A:59-151 Death Domain, Fas                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh....hhhhhhhhhhhhh....................hhhhhhhhh...hhhhhhhhhhhhhh...hhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------T---------------- SAPs(SNPs)
                    PROSITE DAPIN  PDB: A:59-150 UniProt: 1-92                                                          - PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 1pn5 A  59 MAGGAWGRLACYLEFLKKEELKEFQLLLANKAHSRSSSGETPAQPEKTSGMEVASYLVAQYGEQRAWDLALHTWEQMGLRSLCAQAQEGAGHS 151
                                    68        78        88        98       108       118       128       138       148   

Chain A from PDB  Type:PROTEIN  Length:93
 aligned with SPG1_STRSG | P06654 from UniProtKB/Swiss-Prot  Length:448

    Alignment length:141
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150 
           SPG1_STRSG    11 LRKSAFGLASVSAAFLVGSTVFAVDSPIEDTPIIRNGGELTNLLGNSETTLALRNEESATADLTAAAVADTVAAAAAENAGAAAWEAAAAADALAKAKADALKEFNKYGVSDYYKNLINNAKTVEGIKDLQAQVVESAKKA 151
               SCOP domains d1pn5a1 A:59-151           NAL   P1                                                                                                           SCOP domains
               CATH domains 1pn5A00 A:59-151           Dea   th    Domain, Fas                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh....----------hhh---hh---hhhhhhhh....................--hhhhhhhhh...hhhhhhhh-------------hhhhhh..-----------------.hhhhhh........ Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------T--------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pn5 A  59 MAGGAWGRLACYLEFLK----------KEE---LK---EFQLLLANKAHSRSSSGETPAQPEKTSG--MEVASYLVAQYGEQRAWDLA-------------LHTWEQMG-----------------LRSLCAQAQEGAGHS 151
                                    68      |  -       |78   ||   82        92       102     | 110       120       | -         - |      |-         -      |140       150 
                                           75         76 |  79|  81                        108  |                128           129    136               137              
                                                        78   80                               109                                                                        

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1PN5)

(-) Gene Ontology  (28, 28)

NMR Structure(hide GO term definitions)
Chain A   (SPG1_STRSG | P06654)
molecular function
    GO:0019864    IgG binding    Interacting selectively and non-covalently with an immunoglobulin of an IgG isotype.
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A   (NLRP1_HUMAN | Q9C000)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008656    cysteine-type endopeptidase activator activity involved in apoptotic process    Increases the rate of proteolysis catalyzed by a cysteine-type endopeptidase involved in the apoptotic process.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
biological process
    GO:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    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:0051402    neuron apoptotic process    Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
    GO:0050718    positive regulation of interleukin-1 beta secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of interleukin-1 beta from a cell.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0050727    regulation of inflammatory response    Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
    GO:0032495    response to muramyl dipeptide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a muramyl dipeptide stimulus. Muramyl dipeptide is derived from peptidoglycan.
cellular component
    GO:0072558    NLRP1 inflammasome complex    A protein complex that consists of two components, NLRP1 (NALP1) and caspase-1 or caspase-5. The exact mechanisms of NLRP1 activation remain obscure, but potassium ion efflux appears to be essential.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0061702    inflammasome complex    A cytosolic protein complex that is capable of activating caspase-1.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NLRP1_HUMAN | Q9C0003kat 4ifp 4im6
        SPG1_STRSG | P066541em7 1gb1 1igc 1igd 1le3 1mpe 1mvk 1pga 1pgb 1pgx 1q10 2cwb 2den 2gb1 2igd 2igh 2j52 2j53 2ju6 2k0p 2kbt 2klk 2lgi 2mbb 2n7j 2nmq 2plp 2rmm 2rpv 3gb1 3mp9 4kgr 4kgs 4kgt

(-) Related Entries Specified in the PDB File

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