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(-) Description

Authors :  T. Nagata, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 May 04  (Deposition) - 28 Nov 04  (Release) - 24 Feb 09  (Revision)
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Double-Stranded Rna Binding Domain, Dsrbd, Dsrm, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  T. Nagata, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of The N-Terminal Dsrbd From Hypothetical Protein Bab28848
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA HELICASE A
    Expression System PlasmidP021209-25
    Expression System Vector TypePLASMID
    GeneRIKEN CDNA 2810480H04
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 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 1WHQ)

(-) Sites  (0, 0)

(no "Site" information available for 1WHQ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WHQ)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WHQ)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
1DS_RBDPS50137 Double stranded RNA-binding domain (dsRBD) profile.DHX9_MOUSE3-71

(-) Exons   (0, 0)

(no "Exon" information available for 1WHQ)

(-) 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:99
 aligned with DHX9_MOUSE | O70133 from UniProtKB/Swiss-Prot  Length:1380

    Alignment length:137
                              1|  3                                                                                                                                  
                              ||  |  6        16        26        36        46        56        66        76        86        96       106       116       126       
               SCOP domains d1whqa_ A: ATP-dependent RNA helicase A, Dhx9                                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------dsrm-1whqA01 A:4-69                                               ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhh.....eeeeeeee....eeeeeeee.......eeeee..hhhhhhhhhhhhhhhhhhh.................---------------------...-----------------... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------DS_RBD  PDB: A:4-71 UniProt: 3-71                                    -------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                                     6        16        26        36        46        56        66        76        86  |      -         -    | |  -         -    |  
                                                                                                                       89                    90 |                93  

   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  (0, 0)

(no "CATH Domain" information available for 1WHQ)

(-) Pfam Domains  (1, 1)

NMR Structure
Clan: DSRM (45)

(-) Gene Ontology  (28, 28)

NMR Structure(hide GO term definitions)
Chain A   (DHX9_MOUSE | O70133)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004004    ATP-dependent RNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix.
    GO:0008026    ATP-dependent helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0001085    RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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).
biological process
    GO:0070934    CRD-mediated mRNA stabilization    An mRNA stabilization process in which one or more RNA-binding proteins associate with a sequence in the open reading frame called the coding region instability determinant (CRD).
    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:0034605    cellular response to heat    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 heat stimulus, a temperature stimulus above the optimal temperature for that organism.
    GO:0007623    circadian rhythm    Any biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0001649    osteoblast differentiation    The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
    GO:1903608    protein localization to cytoplasmic stress granule    A process in which a protein is transported to, or maintained in, a location within a cytoplasmic stress granule.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
cellular component
    GO:0070937    CRD-mediated mRNA stability complex    A protein complex that binds to, and promotes stabilization of, mRNA molecules containing the coding region instability determinant (CRD). In human, it may consist of IGF2BP1, HNRNPU, SYNCRIP/HNRNPQ, YBX1, and DHX9.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0036464    cytoplasmic ribonucleoprotein granule    A ribonucleoprotein granule located in the cytoplasm.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0097165    nuclear stress granule    A dense aggregation in the nucleus composed of proteins and RNAs that appear when the cell is under stress.
    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)

        DHX9_MOUSE | O701331uil 2rs6 2rs7

(-) Related Entries Specified in the PDB File

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