2F8K | PR0186 - JenaLib

Title :   SEQUENCE SPECIFIC RECOGNITION OF RNA HAIRPINS BY THE SAM DOMAIN OF VTS1

Authors :   T. Aviv, Z. Lin, G. Ben-Ari, C. A. Smibert, F. Sicheri

Date :   02 Dec 05 (Deposition) - 24 Jan 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Vts1-Rna Complex, Sam Domain, Rna Binding Protein- Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Aviv, Z. Lin, G. Ben-Ari, C. A. Smibert, F. Sicheri
Sequence-Specific Recognition Of Rna Hairpins By The Sam Domain Of Vts1P.
Nat. Struct. Mol. Biol. V. 13 168 2006
PubMed-ID: 16429151 | Reference-DOI: 10.1038/NSMB1053

Compounds

*Molecule 1 - 5'-R(UPAPAPUPCPUPUPUPGPAPCPAPGPAPUPU)-3'*
	Chains	:	B
	Engineered	:	YES
	Other Details	:	SRE23
	Synthetic	:	YES

Molecule 2 - PROTEIN VTS1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGEX
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	VTS1
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	VTI1-2 SUPPRESSOR PROTEIN 1

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 (0, 0)

Exons (1, 1)

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

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Chain A from PDB  Type:PROTEIN  Length:84
 aligned with VTS1_YEAST | Q08831 from UniProtKB/Swiss-Prot  Length:523

    Alignment length:84
                                   449       459       469       479       489       499       509       519    
           VTS1_YEAST   440 SSMNPKSLTDPKLLKNIPMWLKSLRLHKYSDALSGTPWIELIYLDDETLEKKGVLALGARRKLLKAFGIVIDYKERDLIDRSAY 523
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:440-523 UniProt: 1-523 [INCOMPLETE]                                 Transcript 1
                 2f8k A 440 SSMNPKSLTDPKLLKNIPMWLKSLRLHKYSDALSGTPWIELIYLDDETLEKKGVLALGARRKLLKAFGIVIDYKERDLIDRSAY 523
                                   449       459       469       479       489       499       509       519

Chain B from PDB  Type:DNA/RNA  Length:16
                                                
                 2f8k B   0 UAAUCUUUGACAGAUU  15
                                     9

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Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (VTS1_YEAST | Q08831)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0070336	flap-structured DNA binding	Interacting selectively and non-covalently with a flap structure in DNA. A DNA flap structure is one in which a single-stranded length of DNA or RNA protrudes from a double-stranded DNA molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0000956	nuclear-transcribed mRNA catabolic process	The chemical reactions and pathways resulting in the breakdown of nuclear-transcribed mRNAs in eukaryotic cells.
	GO:0000289	nuclear-transcribed mRNA poly(A) tail shortening	Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
	GO:0032079	positive regulation of endodeoxyribonuclease activity	Any process that activates or increases the frequency, rate or extent of endodeoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0000932	P-body	A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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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