2XNR - JenaLib

Title :   STRUCTURAL INSIGHTS INTO CIS ELEMENT RECOGNITION OF NON-POLYADENYLATED RNAS BY THE NAB3-RRM

Authors :   B. M. Lunde, M. Horner, A. Meinhart

Date :   05 Aug 10 (Deposition) - 08 Sep 10 (Release) - 16 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Rna Binding Protein-Rna Complex, Transcription Termination, Rna Recognition, Rrm, Rna Processing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. M. Lunde, M. Horner, A. Meinhart
Structural Insights Into Cis Element Recognition Of Non-Polyadenylated Rnas By The Nab3-Rrm.
Nucleic Acids Res. V. 39 337 2011
PubMed-ID: 20805243 | Reference-DOI: 10.1093/NAR/GKQ751

Compounds

Molecule 1 - NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN 3
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3) RIL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RNA RECOGNITION MOTIF, RESIDUES 329-404
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

*Molecule 2 - 5'-R(UPUPCPUPUPAPUPUPCPUPUPA)-3'*
	Chains	:	C
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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)
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Chain A from PDB  Type:PROTEIN  Length:75
 aligned with NAB3_YEAST | P38996 from UniProtKB/Swiss-Prot  Length:802

    Alignment length:75
                                   337       347       357       367       377       387       397     
           NAB3_YEAST   328 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSN 402
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains ----RRM_1-2xnrA01 A:332-395                                         ------- Pfam domains
         Sec.struct. author ...eeee........hhhhhhhhhhhhh.eeeeeee..eeeeee.hhhhhhhhhhhhh..........eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RRM  PDB: A:330-401 UniProt: 330-401                                    - PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 2xnr A 328 MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSN 402
                                   337       347       357       367       377       387       397

Chain C from PDB  Type:DNA/RNA  Length:5
                                     
                 2xnr C   0 UUCUU   4

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 (1, 1)

Gene Ontology (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NAB3_YEAST | P38996)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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).
	GO:0001068	transcription regulatory region RNA binding	Interacting selectively and non-covalently with a RNA region within the transcript that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon.
biological process
	GO:0071034	CUT catabolic process	The chemical reactions and pathways resulting in the breakdown of cryptic unstable transcripts (CUTs).
	GO:0071041	antisense RNA transcript catabolic process	The chemical reactions and pathways resulting in the breakdown of antisense transcripts, i.e. transcripts that were produced from the antisense strand of a gene that produces a gene product and which often have a regulatory effect on the transcription of that gene product.
	GO:0031124	mRNA 3'-end processing	Any process involved in forming the mature 3' end of an mRNA molecule.
	GO:0071028	nuclear mRNA surveillance	The set of processes involved in identifying and degrading defective or aberrant mRNAs within the nucleus.
	GO:0034472	snRNA 3'-end processing	Any process involved in forming the mature 3' end of an snRNA molecule.
	GO:0031126	snoRNA 3'-end processing	Any process involved in forming the mature 3' end of a snoRNA molecule.
	GO:0042780	tRNA 3'-end processing	The process in which the 3' end of a pre-tRNA molecule is converted to that of a mature tRNA.
	GO:0030847	termination of RNA polymerase II transcription, exosome-dependent	The process in which transcription of nonpolyadenylated RNA polymerase II transcripts is terminated; coupled to the maturation of the RNA 3'-end.
cellular component
	GO:0035649	Nrd1 complex	A complex that functions in transcription termination of RNA polymerase II transcribed non-coding RNAs. This complex interacts with the carboxy-terminal domain (CTD) of PolII and the terminator sequences in the nascent RNA transcript. In yeast this complex consists of Nrd1p, Nab3p, and Sen1p.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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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