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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   DROSHA DOUBLE-STRANDED RNA BINDING MOTIF

Authors :   G. A. Mueller, M. Miller, M. Ghosh, E. F. Derose, R. E. London, T. Hall

Date :   13 Apr 09 (Deposition) - 23 Feb 10 (Release) - 21 Mar 12 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (10x)
NMR Structure *: A  (1x)

Keywords :   Drosha, Rna Binding Domain, Hydrolase, Gene Regulation, Nuclear Protein, Gene Regulation, Nuclear Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. A. Mueller, M. T. Miller, E. F. Derose, M. Ghosh, R. E. London, T. M. Hall
Solution Structure Of The Drosha Double-Stranded Rna-Bindin Domain.
Silence V. 1 2 2010
PubMed-ID: 20226070 | Reference-DOI: 10.1186/1758-907X-1-2

Molecule 1 - RIBONUCLEASE 3
	Chains	:	A
	EC Number	:	3.1.26.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21C
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1259-1337
	Gene	:	RNASEN, RN3, RNASE3L
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RIBONUCLEASE III, RNASE III, DROSHA, P241

		1
NMR Structure (10x)	:	A
NMR Structure * (1x)	:	A

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2KHX)

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

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

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DS_RBD	PS50137	Double stranded RNA-binding domain (dsRBD) profile.	RNC_HUMAN	1260-1334	1	A:1260-1334

NMR Structure * (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DS_RBD	PS50137	Double stranded RNA-binding domain (dsRBD) profile.	RNC_HUMAN	1260-1334	1	A:1260-1334

(no "Exon" information available for 2KHX)

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
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Chain A from PDB  Type:PROTEIN  Length:79
 aligned with RNC_HUMAN | Q9NRR4 from UniProtKB/Swiss-Prot  Length:1374

    Alignment length:79
                                  1268      1278      1288      1298      1308      1318      1328         
           RNC_HUMAN   1259 NDPKSQLQQCCLTLRTEGKEPDIPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKYNFPQM 1337
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains --dsrm-2khxA01 A:1261-1332                                                ----- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...........eee...........eeeeeee..ee...eee.hhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -DS_RBD  PDB: A:1260-1334 UniProt: 1260-1334                                --- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                2khx A 1259 NDPKSQLQQCCLTLRTEGKEPDIPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKYNFPQM 1337
                                  1268      1278      1288      1298      1308      1318      1328

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 '\|'

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

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

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DSRM (45)

Family: dsrm (27)

Homo sapiens (Human) (7)

dsrm-2khxA01

A:1261-1332

NMR Structure(hide GO term definitions)

Chain A (RNC_HUMAN | Q9NRR4)

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:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0004521	endoribonuclease activity	Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
	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:0001530	lipopolysaccharide binding	Interacting selectively and non-covalently with lipopolysaccharide.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	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:0006396	RNA processing	Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
	GO:0050829	defense response to Gram-negative bacterium	Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
	GO:0050830	defense response to Gram-positive bacterium	Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
	GO:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
	GO:0010586	miRNA metabolic process	The chemical reactions and pathways involving miRNA, microRNA, a class of single-stranded RNA molecules of about 21-23 nucleotides in length, which regulates gene expression.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0031054	pre-miRNA processing	Any process involved in the conversion of a pre-microRNA transcript into a mature microRNA molecule.
	GO:0031053	primary miRNA processing	Any process involved in the conversion of a primary microRNA transcript into a pre-microRNA molecule.
	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.
	GO:0016075	rRNA catabolic process	The chemical reactions and pathways resulting in the breakdown of rRNA, ribosomal RNA, a structural constituent of ribosomes.
	GO:0010468	regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:2000628	regulation of miRNA metabolic process	Any process that modulates the frequency, rate or extent of miRNA metabolic process.
	GO:0042254	ribosome biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
cellular component
	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: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.

NMR Structure
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