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(-) Description

Title :  SOLUTION STRUCTURE OF DSRM DOMAIN IN DGCR8 PROTEIN
 
Authors :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 May 05  (Deposition) - 14 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Structural Genomics, Dsrm Domain, Dgcr8 Protein, 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 :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of Dsrm Domain In Dgcr8 Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DGCR8 PROTEIN
    Chains: A
    Engineered: YES
    Expression System Plasmid: P040223-57
    Expression System Vector Type: PLASMID
    Fragment: DSRM DOMAIN
    Gene: DGCR8, DGCRK6
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL FREE PROTEIN SYNTHESIS
    Synonym: DIGEORGE SYNDROME CRITICAL REGION 8

 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 1X47)

(-) Sites  (0, 0)

(no "Site" information available for 1X47)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X47)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X47)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X47)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DS_RBDPS50137 Double stranded RNA-binding domain (dsRBD) profile.DGCR8_HUMAN511-578  1A:17-84

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003519891aENSE00001833496chr22:20067755-20067906152DGCR8_HUMAN-00--
1.3bENST000003519893bENSE00001192072chr22:20073210-20074206997DGCR8_HUMAN1-2402400--
1.3fENST000003519893fENSE00001056489chr22:20074685-20074844160DGCR8_HUMAN241-294540--
1.4aENST000003519894aENSE00000879206chr22:20077192-20077334143DGCR8_HUMAN294-341480--
1.4cENST000003519894cENSE00000650862chr22:20077499-20077781283DGCR8_HUMAN342-436950--
1.5ENST000003519895ENSE00000650863chr22:20078958-20079155198DGCR8_HUMAN436-502671A:1-88
1.6ENST000003519896ENSE00000650864chr22:20079392-20079493102DGCR8_HUMAN502-536351A:8-4235
1.7ENST000003519897ENSE00000650865chr22:20080332-2008043099DGCR8_HUMAN536-569341A:42-7534
1.8bENST000003519898bENSE00000650866chr22:20082236-2008231883DGCR8_HUMAN569-596281A:75-9824
1.9aENST000003519899aENSE00000650867chr22:20093700-20093800101DGCR8_HUMAN597-630340--
1.10cENST0000035198910cENSE00000650868chr22:20094115-20094221107DGCR8_HUMAN630-666370--
1.11aENST0000035198911aENSE00000650869chr22:20094794-20094921128DGCR8_HUMAN666-708430--
1.11dENST0000035198911dENSE00000879207chr22:20096413-20096526114DGCR8_HUMAN709-746380--
1.12cENST0000035198912cENSE00001896271chr22:20097548-200993941847DGCR8_HUMAN747-773270--

(-) 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:98
 aligned with DGCR8_HUMAN | Q8WYQ5 from UniProtKB/Swiss-Prot  Length:773

    Alignment length:98
                                   504       514       524       534       544       554       564       574       584        
          DGCR8_HUMAN   495 QDAPTKKEFVINPNGKSEVCILHEYMQRVLKVRPVYNFFECENPSEPFGASVTIDGVTYGSGTASSKKLAKNKAARATLEILIPDFVKQTSEEKPKDS 592
               SCOP domains -------d1x47a1 A:8-92 Dgcr8 protein                                                         ------ SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------dsrm-1x47A01 A:18-82                                             ---------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhh.....eeeeee.......eeeeeee..eeeeeeee..hhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------DS_RBD  PDB: A:17-84 UniProt: 511-578                               -------------- PROSITE
           Transcript 1 (1) Exon 1.5---------------------------------Exon 1.7  PDB: A:42-75            ----------------------- Transcript 1 (1)
           Transcript 1 (2) -------Exon 1.6  PDB: A:8-42              --------------------------------Exon 1.8b  PDB: A:75-98  Transcript 1 (2)
                 1x47 A   1 GSSGSSGEFVINPNGKSEVCILHEYMQRVLKVRPVYNFFECENPSEPFGASVTIDGVTYGSGTASSKKLAKNKAARATLEILIPDFVKQTSESGPSSG  98
                                    10        20        30        40        50        60        70        80        90
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X47)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: DSRM (45)

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (DGCR8_HUMAN | Q8WYQ5)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0070878    primary miRNA binding    Interacting selectively and non-covalently with a primary microRNA (pri-miRNA) transcript, an RNA molecule that is processed into a short hairpin-shaped structure called a pre-miRNA and finally into a functional miRNA. Both double-stranded and single-stranded regions of a pri-miRNA are required for binding.
    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.
    GO:0004525    ribonuclease III activity    Catalysis of the endonucleolytic cleavage of RNA with 5'-phosphomonoesters and 3'-OH termini; makes two staggered cuts in both strands of dsRNA, leaving a 3' overhang of 2 nt.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0031053    primary miRNA processing    Any process involved in the conversion of a primary microRNA transcript into a pre-microRNA molecule.
    GO:0072091    regulation of stem cell proliferation    Any process that modulates the frequency, rate or extent of stem cell proliferation. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070877    microprocessor complex    A protein complex that binds to heme and to pri-miRNAs, and is required for the formation of a pre-microRNA (pre-miRNA), the initial step of microRNA (miRNA) biogenesis. The complex is composed of the double-stranded-RNA-specific RNase Drosha (also called RNASEN) and the RNA-binding protein DGCR8 (heme-free or heme-bound forms). Within the complex, DGCR8 function as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs RNASEN/Drosha to cleave the 3' and 5' strands of a stem-loop to release hairpin-shaped pre-miRNAs.
    GO:0015630    microtubule cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
    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

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        DGCR8_HUMAN | Q8WYQ5: 2yt4 3le4 5b16

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