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(-) Description

Title :  THE SOLUTION STRUCTURE OF THE ADAR2 DSRBM-RNA COMPLEX REVEALS A SEQUENCE-SPECIFIC READ OUT OF THE MINOR GROOVE
 
Authors :  R. Stefl, F. C. Oberstrass, F. H. -T. Allain
Date :  14 Sep 10  (Deposition) - 27 Oct 10  (Release) - 27 Oct 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (19x)
NMR Structure *:  A,B  (1x)
Keywords :  Editing, Dsrna Recognition, Dsrbm, 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 - DOUBLE-STRANDED RNA-SPECIFIC EDITASE 1
    ChainsA
    EC Number3.5.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET30-GB1
    FragmentUNP RESIDUES 74-301
    GeneADARB1, RED1
    Organism CommonBROWN RAT,RAT,RATS
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymDSRNA ADENOSINE DEAMINASE, RNA-EDITING DEAMINASE 1, RNA- EDITING ENZYME 1
 
Molecule 2 - RNA (71-MER)
    ChainsB
    EngineeredYES
    Expression SystemT7 BACTERIOPHAGE
    Expression System Taxid10760
    Organism CommonBROWN RAT,RAT,RATS
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  12
NMR Structure (19x)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 2L3J)

(-) Sites  (0, 0)

(no "Site" information available for 2L3J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2L3J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2L3J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2L3J)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DS_RBDPS50137 Double stranded RNA-binding domain (dsRBD) profile.RED1_RAT78-144
249-298
  2A:5-71
A:176-225
NMR Structure * (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DS_RBDPS50137 Double stranded RNA-binding domain (dsRBD) profile.RED1_RAT78-144
249-298
  2A:5-71
A:176-225

(-) Exons   (0, 0)

(no "Exon" information available for 2L3J)

(-) 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:236
 aligned with RED1_RAT | P51400 from UniProtKB/Swiss-Prot  Length:711

    Alignment length:236
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303      
             RED1_RAT    74 PGPVLPKNALMQLNEIKPGLQYMLLSQTGPVHAPLFVMSVEVNGQVFEGSGPTKKKAKLHAAEKALRSFVQFPNASEAHLAMGRTLSVNTDFTSDQADFPDTLFNGFETPDKSEPPFYVGSNGDDSFSSSGDVSLSASPVPASLTQPPLPIPPPFPPPSGKNPVMILNELRPGLKYDFLSESGESHAKSFVMSVVVDGQFFEGSGRNKKLAKARAAQSALATVFNLHLDQTPSRQP 309
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------dsrm-2l3jA01 A:163-223                                       ------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------dsrm-2l3jA02 A:163-223                                       ------------- Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhhh...eeeeeeee......eeeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhh...........................................................................................hhhhhhhhhh..eeeeee..........eeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----DS_RBD  PDB: A:5-71 UniProt: 78-144                                --------------------------------------------------------------------------------------------------------DS_RBD  PDB: A:176-225 UniProt: 249-298           ----------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2l3j A   1 PGPVLPKNALMQLNEIKPGLQYMLLSQTGPVHAPLFVMSVEVNGQVFEGSGPTKKKAKLHAAEKALRSFVQFPNASEAHLAMGRTLSVNTDFTSDQADFPDTLFNGFETPDKSEPPFYVGSNGDDSFSSSGDVSLSASPVPASLTQPPLPIPPPFPPPSGKNPVMILNELRPGLKYDFLSESGESHAKSFVMSVVVDGQFFEGSGRNKKLAKARAAQSALATVFNLHLLEHHHHHH 236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      

Chain B from PDB  Type:RNA  Length:71
                                                                                                       
                 2l3j B 237 GGCAUUAAGGUGGGUGGAAUAGUAUAACAAUAUGCUAAAUGUUGUUAUAGUAUCCCACCUACCCUGAUGCC 307
                                   246       256       266       276       286       296       306 

   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 2L3J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2L3J)

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Clan: DSRM (45)
(-)
Family: dsrm (27)

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (RED1_RAT | P51400)
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.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
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:0016553    base conversion or substitution editing    Any base modification or substitution events that result in alterations in the coding potential or structural properties of RNAs as a result of changes in the base-pairing properties of the modified ribonucleoside(s).
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0016556    mRNA modification    The covalent alteration of one or more nucleotides within an mRNA molecule to produce an mRNA molecule with a sequence that differs from that coded genetically.
    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:0050685    positive regulation of mRNA processing    Any process that activates or increases the frequency, rate or extent of mRNA processing.
    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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        RED1_RAT | P514002b7t 2b7v 2l3c

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