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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN DGCR8 CORE
 
Authors :  Y. Cho, S. Y. Sohn
Date :  05 Apr 07  (Deposition) - 21 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Dsrbd, Rna Binding Domain, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Y. Sohn, W. J. Bae, J. J. Kim, K. H. Yeom, V. N. Kim, Y. Cho
Crystal Structure Of Human Dgcr8 Core
Nat. Struct. Mol. Biol. V. 14 847 2007
PubMed-ID: 17704815  |  Reference-DOI: 10.1038/NSMB1294
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN DGCR8
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentTWO DSRBDS AND C-TERMINAL DOMAIN
    GeneDGCR8, C22ORF12, DGCRK6
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    StrainHEK293T
    SynonymDIGEORGE SYNDROME CRITICAL REGION 8, DIGEORGE SYNDROME CHROMOSOMAL REGION

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2YT4)

(-) Sites  (0, 0)

(no "Site" information available for 2YT4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YT4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YT4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YT4)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DS_RBDPS50137 Double stranded RNA-binding domain (dsRBD) profile.DGCR8_HUMAN511-578  1A:511-578

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 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:489-502 (gaps)26
1.6ENST000003519896ENSE00000650864chr22:20079392-20079493102DGCR8_HUMAN502-536351A:502-53635
1.7ENST000003519897ENSE00000650865chr22:20080332-2008043099DGCR8_HUMAN536-569341A:536-56934
1.8bENST000003519898bENSE00000650866chr22:20082236-2008231883DGCR8_HUMAN569-596281A:569-596 (gaps)28
1.9aENST000003519899aENSE00000650867chr22:20093700-20093800101DGCR8_HUMAN597-630341A:597-63034
1.10cENST0000035198910cENSE00000650868chr22:20094115-20094221107DGCR8_HUMAN630-666371A:630-666 (gaps)37
1.11aENST0000035198911aENSE00000650869chr22:20094794-20094921128DGCR8_HUMAN666-708431A:666-70136
1.11dENST0000035198911dENSE00000879207chr22:20096413-20096526114DGCR8_HUMAN709-746380--
1.12cENST0000035198912cENSE00001896271chr22:20097548-200993941847DGCR8_HUMAN747-773270--

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:196
 aligned with DGCR8_HUMAN | Q8WYQ5 from UniProtKB/Swiss-Prot  Length:773

    Alignment length:225
                                   486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696     
          DGCR8_HUMAN   477 ESERPILPANQKLITLSVQDAPTKKEFVINPNGKSEVCILHEYMQRVLKVRPVYNFFECENPSEPFGASVTIDGVTYGSGTASSKKLAKNKAARATLEILIPDFVKQTSEEKPKDSEELEYFNHISIEDSRVYELTSKAGLLSPYQILHECLKRNHGMGDTSIKFEVVPGKNQKSEYVMACGKHTVRGWCKNKRVGKQLASQKILQLLHPHVKNWGSLLRMYGRE 701
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --            ------   ------------------------------------------------------------------------------------        ----------------------------dsrm-2yt4A01 A:620-684                                           ----------------- Pfam domains (1)
           Pfam domains (2) --            ------   ------------------------------------------------------------------------------------        ----------------------------dsrm-2yt4A02 A:620-684                                           ----------------- Pfam domains (2)
         Sec.struct. author ..------------.eeee.---..eeee.....hhhhhhhhhhhhh.....eeeeee.......eeeeeee..eeeeeeee.hhhhhhhhhhhhhhhhhh......--------.hhhhhhhhh.....hhhhhhhhhh..hhhhhhhhhhhh......eeee..------..eeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhh....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------DS_RBD  PDB: A:511-578 UniProt: 511-578                             --------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5 UniProt: 436-502 ---------------------------------Exon 1.7  PDB: A:536-569          ------------------------------------------------------------Exon 1.10c  PDB: A:630-666 (gaps)    ----------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.6  PDB: A:502-536           --------------------------------Exon 1.8b UniProt: 569-596  Exon 1.9a  PDB: A:597-630         -----------------------------------Exon 1.11a  PDB: A:666-701           Transcript 1 (2)
                 2yt4 A 489 GS------------HMSVQD---KKEFVINPNGKSEVCILHEYMQRVLKVRPVYNFFECENPSEPFGASVTIDGVTYGSGTASSKKLAKNKAARATLEILIPDFVKQ--------SEELEYFNHISIEDSRVYELTSKAGLLSPYQILHECLKRNHGMGDTSIKFE------QKSEYVMACGKHTVRGWCKNKRVGKQLASQKILQLLHPHVKNWGSLLRMYGRE 701
                             |       -    |  496   |   506       516       526       536       546       556       566       576      |  -     | 596       606       616       626       636     |   -  |    656       666       676       686       696     
                             |          491  496 500                                                                                583      592                                               642    649                                                    
                           490                                                                                                                                                                                                                               

   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 2YT4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YT4)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: DSRM (45)
(-)
Family: dsrm (27)
1adsrm-2yt4A01A:620-684
1bdsrm-2yt4A02A:620-684

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(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

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

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        DGCR8_HUMAN | Q8WYQ51x47 3le4 5b16

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