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(-) Description

Title :  SOLUTION STRUCTURE OF THE SECOND KH DOMAIN IN RING FINGER AND KH DOMAIN CONTAINING PROTEIN 1
 
Authors :  C. Abe, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  15 Mar 06  (Deposition) - 15 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Kh Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Abe, Y. Muto, M. Inoue, T. Terada, T. Kigawa, M. Shirouzu, S. Yokoyama
Solution Structure Of The Second Kh Domain In Ring Finger And Kh Domain Containing Protein 1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RING FINGER AND KH DOMAIN-CONTAINING PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: CELL FREE SYNTHESIS
    Expression System Plasmid: P050829-12
    Expression System Vector Type: PLASMID
    Fragment: K HOMOLOGY DOMAIN
    Gene: RKHD1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS

 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 2DGR)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KH_TYPE_1PS50084 Type-1 KH domain profile.MEX3D_HUMAN188-240
273-334		  1-
A:107-168

(-) Exons   (0, 0)

(no "Exon" information available for 2DGR)

(-) 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:83
 aligned with MEX3D_HUMAN | Q86XN8 from UniProtKB/Swiss-Prot  Length:651

    Alignment length:100
                                   268       278       288       298       308       318       328       338       348       358
          MEX3D_HUMAN   259 GLPGAAQGPPNLPGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVTGMPENVDRAREEIEAHITLRTGAFTDAGPDSDFHANG 358
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......-.-----..eeeeee.hhhhhhhhhh....hhhhhhhhh..eee........eeeeee...hhhhhhhhhhhhhhh..------....-----. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------KH_TYPE_1  PDB: A:107-168 UniProt: 273-334                    ------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 2dgr A  99 GSSGSS-G-----GQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVTGMPENVDRAREEIEAHITLRS------GPSS-----G 181
                                 | | -   |   112       122       132       142       152       162       172   |     -|  |   181
                               104 |   106                                                                   176    177  |   181
                                 105                                                                                   180
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

NMR Structure(hide GO term definitions)
Chain A   (MEX3D_HUMAN | Q86XN8)
molecular function
    GO:0017091    AU-rich element binding    Interacting selectively and non-covalently with a region of RNA containing frequent adenine and uridine bases.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0061157    mRNA destabilization    Any process that decreases the stability of an mRNA molecule, making it more vulnerable to degradative processes. Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
    GO:0010609    mRNA localization resulting in posttranscriptional regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression after the production of a mRNA transcript by its transport into, or maintainance in, a specific location within the cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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