Show PDB file:   
         Plain Text   HTML   (compressed file size)
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - manually
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - manually
NMR Structure - manually  (Jmol Viewer)
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Authors :  R. Stefl, M. Xu, L. Skrisovska, R. B. Emeson, F. H. -T. Allain
Date :  05 Oct 05  (Deposition) - 14 Mar 06  (Release) - 24 Feb 09  (Revision)
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Rna Editing, Rna-Binding Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  R. Stefl, M. Xu, L. Skrisovska, R. B. Emeson, F. H. -T. Allain
Structure And Specific Rna Binding Of Adar2 Double-Stranded Rna Binding Motifs.
Structure V. 14 345 2006
PubMed-ID: 16472753  |  Reference-DOI: 10.1016/J.STR.2005.11.013
(for further references see the PDB file header)

(-) Compounds

    EC Number3.5.-.-
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET16
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneADARB1, RED1
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 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 2B7V)

(-) Sites  (0, 0)

(no "Site" information available for 2B7V)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B7V)

(-) Cis Peptide Bonds  (8, 14)

NMR Structure
11, 5, 7, 17Gly A:26 -Glu A:27
22Ser A:25 -Gly A:26
311, 14, 15Pro A:1 -Ser A:2
412Ser A:28 -His A:29
514His A:29 -Ala A:30
615, 16Ala A:30 -Lys A:31
718Gly A:3 -Lys A:4
820Ser A:2 -Gly A:3

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B7V)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
1DS_RBDPS50137 Double stranded RNA-binding domain (dsRBD) profile.RED1_RAT78-144

(-) Exons   (0, 0)

(no "Exon" information available for 2B7V)

(-) 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:71
 aligned with RED1_RAT | P51400 from UniProtKB/Swiss-Prot  Length:711

    Alignment length:71
                                   240       250       260       270       280       290       300 
               SCOP domains d2b7va1 A:1-71 dsRNA-specific editase 1                                 SCOP domains
               CATH domains 2b7vA00 A:1-71  [code=, no name defined]                     CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh...eeeeee.........eeeeee....eeeeee.hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------DS_RBD  PDB: A:19-68 UniProt: 249-298             --- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                                    10        20        30        40        50        60        70 

   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
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B7V)

(-) 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.


(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2b7v)
(no "Sites" information available for 2b7v)
  Cis Peptide Bonds
    Ala A:30 - Lys A:31   [ RasMol ]  
    Gly A:26 - Glu A:27   [ RasMol ]  
    Gly A:3 - Lys A:4   [ RasMol ]  
    His A:29 - Ala A:30   [ RasMol ]  
    Pro A:1 - Ser A:2   [ RasMol ]  
    Ser A:2 - Gly A:3   [ RasMol ]  
    Ser A:25 - Gly A:26   [ RasMol ]  
    Ser A:28 - His A:29   [ RasMol ]  

(-) Still Images

  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
Access by UniProt ID/Accession number
  RED1_RAT | P51400
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
Access by Enzyme Classificator   (EC Number)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
Access by UniProt ID/Accession number
  RED1_RAT | P51400
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

        RED1_RAT | P514002b7t 2l3c 2l3j

(-) Related Entries Specified in the PDB File