1DI2 | PR0020 - JenaLib

Title :   CRYSTAL STRUCTURE OF A DSRNA-BINDING DOMAIN COMPLEXED WITH DSRNA: MOLECULAR BASIS OF DOUBLE-STRANDED RNA-PROTEIN INTERACTIONS

Authors :   J. M. Ryter, S. C. Schultz

Date :   28 Nov 99 (Deposition) - 02 Dec 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C,D,E,G
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: E  (2x)
Biol. Unit 3: G  (2x)

Keywords :   Protein-Rna Complex, Double Stranded Rna, Protein-Rna Interactions, Rna-Bining Protein, Rna Binding Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Ryter, S. C. Schultz
Molecular Basis Of Double-Stranded Rna-Protein Interactions: Structure Of A Dsrna-Binding Domain Complexed With Dsrna.
Embo J. V. 17 7505 1998
PubMed-ID: 9857205 | Reference-DOI: 10.1093/EMBOJ/17.24.7505
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DS_RBD	PS50137	Double stranded RNA-binding domain (dsRBD) profile.	PRKAB_XENLA	20-87 112-180 225-293	2	- A:113-180 B:113-180 -

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DS_RBD	PS50137	Double stranded RNA-binding domain (dsRBD) profile.	PRKAB_XENLA	20-87 112-180 225-293	2	- A:113-180 B:113-180 -

Biological Unit 2 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DS_RBD	PS50137	Double stranded RNA-binding domain (dsRBD) profile.	PRKAB_XENLA	20-87 112-180 225-293	0	- - - -

Biological Unit 3 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DS_RBD	PS50137	Double stranded RNA-binding domain (dsRBD) profile.	PRKAB_XENLA	20-87 112-180 225-293	0	- - - -

Exons (0, 0)

Sequences/Alignments

Asymmetric 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:69
 aligned with PRKAB_XENLA | Q91836 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:72
                                   118       128       138       148       158       168       178  
          PRKAB_XENLA   109 MQENPVGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVETFVETGSGTSKQVAKRVAAEKLLTKFKT 180
               SCOP domains d   1di2a_ A: Double-stranded RNA-binding protein A, second dsRBD        SCOP domains
               CATH domains 1   di2A00 A:112-180  [code=3.30.160.20, no name defined]                CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author h---hhhhhhhhhhhhh....eeeeeeee.hhhhheeeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---DS_RBD  PDB: A:113-180 UniProt: 112-180                               PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 1di2 A 112 M---PVGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVETFVETGSGTSKQVAKRVAAEKLLTKFKT 180
                            |   |  118       128       138       148       158       168       178  
                            | 113                                                                   
                          112

Chain B from PDB  Type:PROTEIN  Length:60
 aligned with PRKAB_XENLA | Q91836 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:72
                                   118       128       138       148       158       168       178  
          PRKAB_XENLA   109 MQENPVGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVETFVETGSGTSKQVAKRVAAEKLLTKFKT 180
               SCOP domains d   1di2b_ B: Double-strand         ed RNA-binding protein A, second dsR SCOP domains
               CATH domains 1   di2B00 B:112-180  [code         =3.30.160.20, no name defined]       CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author h---hhhhhhhhhhhhh....ee....---------.eeeeee..eeeeee..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---DS_RBD  PDB: B:113-180 UniProt: 112-180                               PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 1di2 B 112 M---PVGSLQELAVQKGWRLPEYTVAQ---------FTITCRVETFVETGSGTSKQVAKRVAAEKLLTKFKT 180
                            |   |  118       128      |  -      |148       158       168       178  
                          112 113                   135       145

Chain C from PDB  Type:RNA  Length:10
                                          
                 1di2 C   1 GGCGCGCGCC  10
                                    10

Chain D from PDB  Type:RNA  Length:10
                                          
                 1di2 D  11 GGCGCGCGCC  20
                                    20

Chain E from PDB  Type:RNA  Length:10
                                          
                 1di2 E  21 GGCGCGCGCC  30
                                    30

Chain G from PDB  Type:RNA  Length:10
                                          
                 1di2 G  41 GGCGCGCGCC  50
                                    50

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, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PRKAB_XENLA | Q91836)

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:0008047	enzyme activator activity	Binds to and increases the activity of an enzyme.
biological process
	GO:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
	GO:0043085	positive regulation of catalytic activity	Any process that activates or increases the activity of an enzyme.
	GO:0030422	production of siRNA involved in RNA interference	Cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of RNA interference.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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: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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