2CJK - JenaLib

Title :   STRUCTURE OF THE RNA BINDING DOMAIN OF HRP1 IN COMPLEX WITH RNA

Authors :   J. M. Perez-Canadillas

Date :   04 Apr 06 (Deposition) - 28 Jun 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (25x)

Keywords :   Hrp1, Rna-Binding, Rna Processing, Mrna Processing, Nonsense-Mediated Mrna Decay, Cleavage, Polyadenylation, Nuclear Protein, Rna-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Perez-Canadillas
Grabbing The Message: Structural Basis Of Mrna 3'Utr Recognition By Hrp1.
Embo J. V. 25 3167 2006
PubMed-ID: 16794580 | Reference-DOI: 10.1038/SJ.EMBOJ.7601190

Compounds

Molecule 1 - NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN 4
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	RNA-BINDING DOMAIN, RESIDUES 156-322
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	HRP1, CLEAVAGE FACTOR IB, CFIB

*Molecule 2 - 5'-R(UPAPUPAPUPAPUPAP)-3'*
	Chains	:	B
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	POLYADENYLATION ENHANCEMENT ELEMENT
	Synthetic	:	YES

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)

Exons (1, 1)

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)
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Chain A from PDB  Type:PROTEIN  Length:167
 aligned with HRP1_YEAST | Q99383 from UniProtKB/Swiss-Prot  Length:534

    Alignment length:167
                                   165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       
           HRP1_YEAST   156 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPRH 322
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.......hhhhhhhhhh....eeeee.............eeeee..hhhhhhhhhh........eeee...hhhhhhhheeeeeeee....hhhhhhhhhhh.....eee...........eeeeeee.hhhhhhhhhhh.........eeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---RRM  PDB: A:159-241 UniProt: 159-241                                               -RRM  PDB: A:243-320 UniProt: 243-320                                          -- PROSITE
               Transcript 1 Exon 1.1  PDB: A:156-322 UniProt: 1-534 [INCOMPLETE]                                                                                                                    Transcript 1
                 2cjk A 156 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPRH 322
                                   165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315

Chain B from PDB  Type:RNA  Length:8
                                        
                 2cjk B   1 UAUAUAUA   8

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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (14, 14)

NMR Structure(hide GO term definitions)

Chain A (HRP1_YEAST | Q99383)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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.
	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).
biological process
	GO:0006378	mRNA polyadenylation	The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
	GO:0098789	pre-mRNA cleavage required for polyadenylation	The targeted, endonucleolytic cleavage of a pre-mRNA, required for polyadenylation of the 3' end. This cleavage is directed by binding sites near the 3' end of the mRNA and leaves a 3' hydoxyl end which then becomes a target for adenylation.
	GO:0072423	response to DNA damage checkpoint signaling	A process that occurs in response to signals generated as a result of DNA damage checkpoint signaling.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0010494	cytoplasmic stress granule	A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
	GO:0005849	mRNA cleavage factor complex	Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules.
	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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