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(-) Description

Title :  OVINE PRION PROTEIN VARIANT R168
 
Authors :  B. Christen, D. A. Lysek, T. Herrmann, K. Wuthrich
Date :  23 Nov 04  (Deposition) - 28 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Prion Protein, Sheep, Ovprp, Polymorphism, Scrapie, Tse, Glycoprotein, Gpi-Anchor, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. A. Lysek, C. Schorn, L. G. Nivon, V. Esteve-Moya, B. Christen, L. Calzolai, C. Von Schroetter, F. Fiorito, T. Herrmann, P. Guntert, K. Wuthrich
Prion Protein Nmr Structures Of Cats, Dogs, Pigs, And Sheep
Proc. Natl. Acad. Sci. Usa V. 102 640 2005
PubMed-ID: 15647367  |  Reference-DOI: 10.1073/PNAS.0408937102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MAJOR PRION PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPRSETA
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentGLOBULAR DOMAIN, RESIDUES 121-231
    GenePRNP
    Organism CommonSHEEP
    Organism ScientificOVIS ARIES
    Organism Taxid9940
    SynonymPRP

 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 1Y2S)

(-) Sites  (0, 0)

(no "Site" information available for 1Y2S)

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:179 -A:214

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y2S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (7, 7)

NMR Structure (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PRIO_SHEEP_002 *A136VPRIO_SHEEP  ---  ---AA133V
2UniProtVAR_PRIO_SHEEP_003 *M137TPRIO_SHEEP  ---  ---AM134T
3UniProtVAR_PRIO_SHEEP_004 *L141FPRIO_SHEEP  ---  ---AL138F
4UniProtVAR_PRIO_SHEEP_005 *R154HPRIO_SHEEP  ---  ---AR151H
5UniProtVAR_PRIO_SHEEP_006 *R171HPRIO_SHEEP  ---  ---AR168H
6UniProtVAR_PRIO_SHEEP_007 *R171QPRIO_SHEEP  ---  ---AR168Q
7UniProtVAR_PRIO_SHEEP_008 *R211QPRIO_SHEEP  ---  ---AR208Q
   * ID not provided by source

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PRION_2PS00706 Prion protein signature 2.PRIO_SHEEP203-221  1A:200-218

(-) Exons   (0, 0)

(no "Exon" information available for 1Y2S)

(-) 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:113
 aligned with PRIO_SHEEP | P23907 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:113
                                   131       141       151       161       171       181       191       201       211       221       231   
           PRIO_SHEEP   122 GAVVGGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDRYSNQNNFVHDCVNITVKQHTVTTTTKGENFTETDIKIMERVVEQMCITQYQRESQAYYQRGAS 234
               SCOP domains d1y2sa_ A: Prion protein domain                                                                                   SCOP domains
               CATH domains 1y2sA00 A:119-231 Major Prion Protein                                                                             CATH domains
               Pfam domains ---------------Prion-1y2sA01 A:134-231                                                                            Pfam domains
         Sec.struct. author .....hhhhhee.............hhhhhhhhhhh.......ee........hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhh... Sec.struct. author
             SAPs(SNPs) (1) --------------VT---F------------H----------------H---------------------------------------Q----------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------Q--------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ---------------------------------------------------------------------------------PRION_2            ------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1y2s A 119 GSVVGGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDRYSNQNNFVHDCVNITVKQHTVTTTTKGENFTETDIKIMERVVEQMCITQYQRESQAYYQRGAS 231
                                   128       138       148       158       168       178       188       198       208       218       228   

   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  (1, 1)

NMR Structure

(-) Gene Ontology  (29, 29)

NMR Structure(hide GO term definitions)
Chain A   (PRIO_SHEEP | P23907)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    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:0015631    tubulin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of tubulin, including microtubules.
biological process
    GO:0071280    cellular response to copper ion    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a copper ion stimulus.
    GO:0035690    cellular response to drug    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0050860    negative regulation of T cell receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0046007    negative regulation of activated T cell proliferation    Any process that stops, prevents or reduces the rate or extent of activated T cell proliferation.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0070885    negative regulation of calcineurin-NFAT signaling cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of the calcineurin-NFAT signaling cascade.
    GO:0032689    negative regulation of interferon-gamma production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:0032700    negative regulation of interleukin-17 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines.
    GO:0032703    negative regulation of interleukin-2 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-2 production.
    GO:0001933    negative regulation of protein phosphorylation    Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
    GO:0043433    negative regulation of sequence-specific DNA binding transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:1901379    regulation of potassium ion transmembrane transport    Any process that modulates the frequency, rate or extent of potassium ion transmembrane transport.
    GO:0032880    regulation of protein localization    Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
    GO:0006979    response to oxidative stress    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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0031225    anchored component of membrane    The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PRIO_SHEEP | P239071g04 1m25 1s4t 1tpx 1tqb 1tqc 1uw3 1xyu 2ktm 2mv8 2mv9 2n53 2rmv 2rmw

(-) Related Entries Specified in the PDB File

1xyu OVINE PRION PROTEIN VARIANT H168