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(-) Description

Title :  SOLUTION NMR STRUCTURE OF THE R/G STEM LOOP RNA-ADAR2 DSRBM2 COMPLEX
 
Authors :  F. H. -T. Allain, F. C. Oberstrass, R. Stefl
Date :  20 Aug 10  (Deposition) - 27 Oct 10  (Release) - 27 Oct 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Ac Mismatch, Rna Editing, Dsrbm, Stemloop, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Stefl, F. C. Oberstrass, J. L. Hood, M. Jourdan, M. Zimmermann, L. Skrisovska, C. Maris, L. Peng, C. Hofr, R. B. Emeson, F. H. Allain
The Solution Structure Of The Adar2 Dsrbm-Rna Complex Reveals A Sequence-Specific Readout Of The Minor Groove.
Cell(Cambridge, Mass. ) V. 143 225 2010
PubMed-ID: 20946981  |  Reference-DOI: 10.1016/J.CELL.2010.09.026

(-) Compounds

Molecule 1 - ADENOSINE DEAMINASE
    ChainsB
    EC Number3.5.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)+RIL
    Expression System Taxid469008
    Expression System VectorPET16
    FragmentUNP RESIDUES 231-301
    GeneADAR2, ADARB1, MCG_3378, RED1
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymRNA-SPECIFIC, B1, ISOFORM CRA_D
 
Molecule 2 - RNA (42-MER)
    ChainsA
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
NMR Structure (20x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2L2K)

(-) Sites  (0, 0)

(no "Site" information available for 2L2K)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2L2K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2L2K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2L2K)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DS_RBDPS50137 Double stranded RNA-binding domain (dsRBD) profile.RED1_MOUSE78-144
249-298
  1-
B:61-110
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DS_RBDPS50137 Double stranded RNA-binding domain (dsRBD) profile.RED1_MOUSE78-144
249-298
  1-
B:61-110

(-) Exons   (0, 0)

(no "Exon" information available for 2L2K)

(-) 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:42
                                                                          
                 2l2k A   1 GGUAAGGUGGGUGGAAUCCUUCGGGAUCCCACCUACCCUGCC  42
                                    10        20        30        40  

Chain B from PDB  Type:PROTEIN  Length:71
 aligned with RED1_MOUSE | Q91ZS8 from UniProtKB/Swiss-Prot  Length:711

    Alignment length:71
                                   240       250       260       270       280       290       300 
           RED1_MOUSE   231 PSGKNPVMILNELRPGLKYDFLSESGESHAKSFVMSVVVDGQFFEGSGRNKKLAKARAAQSALATVFNLHL 301
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh...eeeeeeee......eeeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------DS_RBD  PDB: B:61-110 UniProt: 249-298            --- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 2l2k B  43 PSGKNPVMILNELRPGLKYDFLSESGESHAKSFVMSVVVDGQFFEGSGRNKKLAKARAAQSALATVFNLHL 113
                                    52        62        72        82        92       102       112 

   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 2L2K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2L2K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2L2K)

(-) Gene Ontology  (18, 18)

NMR Structure(hide GO term definitions)
Chain B   (RED1_MOUSE | Q91ZS8)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004000    adenosine deaminase activity    Catalysis of the reaction: adenosine + H2O = inosine + NH3.
    GO:0003726    double-stranded RNA adenosine deaminase activity    Catalysis of the reaction: adenosine + H2O = inosine + NH3, in a double-stranded RNA molecule.
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0006382    adenosine to inosine editing    The conversion of an adenosine residue to inosine in an RNA molecule by deamination.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0030336    negative regulation of cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0044387    negative regulation of protein kinase activity by regulation of protein phosphorylation    The stopping, prevention, or reduction in frequency, rate or extent of protein kinase activity as a result of regulating the phosphorylation status of that protein kinase.
    GO:0045070    positive regulation of viral genome replication    Any process that activates or increases the frequency, rate or extent of viral genome replication.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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