2L41 - JenaLib

Title :   NAB3 RRM - UCUU COMPLEX

Authors :   R. Stefl, R. Pergoli, F. Hobor, K. Kubicek, M. Zimmermann, J. Pasulka, C

Date :   28 Sep 10 (Deposition) - 17 Nov 10 (Release) - 30 May 12 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)
NMR Structure *: A,B  (1x)

Keywords :   Nab3 Rrm, Ucuu Oligonucleotide, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Hobor, R. Pergoli, K. Kubicek, D. Hrossova, V. Bacikova, M. Zimmermann, J. Pasulka, C. Hofr, S. Vanacova, R. Stefl
Recognition Of Transcription Termination Signal By The Nuclear Polyadenylated Rna-Binding (Nab) 3 Protein
J. Biol. Chem. V. 286 3645 2011
PubMed-ID: 21084293 | Reference-DOI: 10.1074/JBC.M110.158774

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, 1)

Exons (0, 0)

Sequences/Alignments

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:77
 aligned with NAB3_YEAST | P38996 from UniProtKB/Swiss-Prot  Length:802

    Alignment length:77
                                   337       347       357       367       377       387       397       
           NAB3_YEAST   328 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNAR 404
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----RRM_1-2l41A01 A:5-68                                            --------- Pfam domains
         Sec.struct. author ..eeeee........hhhhhhhhh.......eee......eeee.hhhhhhhhhhhhh..........eeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RRM  PDB: A:3-74 UniProt: 330-401                                       --- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 2l41 A   1 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNAR  77
                                    10        20        30        40        50        60        70

Chain B from PDB  Type:RNA  Length:4
                                    
                 2l41 B  78 UCUU  81

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Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (17, 17)

NMR Structure(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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