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(-) Description

Title :  REFINED STRUCTURE OF RNA APTAMER IN COMPLEX WITH THE PARTIAL BINDING PEPTIDE OF PRION PROTEIN
 
Authors :  T. Hayashi, H. Oshima, T. Mashima, T. Nagata, M. Katahira, M. Kinoshita
Date :  24 Dec 13  (Deposition) - 21 May 14  (Release) - 21 May 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C,D  (5x)
NMR Structure *:  A,B,C,D  (1x)
Keywords :  Aptamer, Prion, Rna, Alzheimer'S Disease, Membrane Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Hayashi, H. Oshima, T. Mashima, T. Nagata, M. Katahira, M. Kinoshit
Binding Of An Rna Aptamer And A Partial Peptide Of A Prion Protein: Crucial Importance Of Water Entropy In Molecular Recognition
Nucleic Acids Res. 2014
PubMed-ID: 24803670  |  Reference-DOI: 10.1093/NAR/GKU382

(-) Compounds

Molecule 1 - RNA_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')
    ChainsA, B
    EngineeredYES
    SyntheticYES
 
Molecule 2 - P16 PEPTIDE FROM MAJOR PRION PROTEIN
    ChainsC, D
    EngineeredYES
    Organism CommonBOVINE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    Other DetailsSYNTHETIC PEPTIDE
    SynonymPRP, MAJOR SCRAPIE-ASSOCIATED FIBRIL PROTEIN 1
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
NMR Structure (5x)ABCD
NMR Structure * (1x)ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2RU7)

(-) Sites  (0, 0)

(no "Site" information available for 2RU7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RU7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RU7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RU7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RU7)

(-) Exons   (1, 2)

NMR Structure (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000402921ENSBTAE00000340808chr13:47214467-4721451953PRIO_BOVIN-00--
1.2ENSBTAT000000402922ENSBTAE00000340806chr13:47216955-4721705298PRIO_BOVIN-00--
1.3ENSBTAT000000402923ENSBTAE00000310243chr13:47230279-472343694091PRIO_BOVIN1-2682682C:25-36
D:37-48
12
12

(-) 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:RNA  Length:12
                                            
                 2ru7 A   1 GGAGGAGGAGGA  12
                                    10  

Chain B from PDB  Type:RNA  Length:12
                                            
                 2ru7 B  13 GGAGGAGGAGGA  24
                                    22  

Chain C from PDB  Type:PROTEIN  Length:12
 aligned with PRIO_BOVIN | P10279 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:12
                                   117  
           PRIO_BOVIN   108 GQWNKPSKPKTN 119
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
               Transcript 1 Exon 1.3     Transcript 1
                 2ru7 C  25 GQWNKPSKPKTN  36
                                    34  

Chain D from PDB  Type:PROTEIN  Length:12
 aligned with PRIO_BOVIN | P10279 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:12
                                   117  
           PRIO_BOVIN   108 GQWNKPSKPKTN 119
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
               Transcript 1 Exon 1.3     Transcript 1
                 2ru7 D  37 GQWNKPSKPKTN  48
                                    46  

   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  (0, 0)

(no "SCOP Domain" information available for 2RU7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2RU7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2RU7)

(-) Gene Ontology  (29, 29)

NMR Structure(hide GO term definitions)
Chain C,D   (PRIO_BOVIN | P10279)
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_BOVIN | P102791dwy 1dwz 1dx0 1dx1 1skh 2hh0 2rsk 4yx2

(-) Related Entries Specified in the PDB File

2rsk RELATED ID: 11489 RELATED DB: BMRB