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(-) Description

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 :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Rna Binding Protein, Transcription Termination, Rna Processing, Rna Recognition, Rrm (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

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CAF1Mod. Amino AcidS-DIMETHYLARSINOYL-CYSTEINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:326 , PRO A:374 , ASN A:389 , PHE A:390 , HOH A:2076 , ARG A:331 , LYS A:363 , PHE A:366 , PHE A:368BINDING SITE FOR RESIDUE ACT A1405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.NAB3_YEAST330-401  1A:330-401

(-) Exons   (0, 0)

(no "Exon" information available for 2XNQ)

(-) 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)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:79
 aligned with NAB3_YEAST | P38996 from UniProtKB/Swiss-Prot  Length:802

    Alignment length:84
                                   330       340       350       360       370       380       390       400    
           NAB3_YEAST   321 TEMHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNAR 404
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------RRM_1-2xnqA01 A:332-395                                         --------- Pfam domains
         Sec.struct. author ...-----..eeeee.......hhhhhhhhhhhhh.eeeeee...eeeeee.hhhhhhhhhhhhh..ee..ee.eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------RRM  PDB: A:330-401 UniProt: 330-401                                    --- PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 2xnq A 326 SHM-----KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIEcESQEMNFGKKLILEVSSSNAR 404
                              |    330       340       350       360       370       380  |    390       400    
                              |   329                                                   383-CAF                 
                            328
   Legend:   → Mismatch (orange background)
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  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)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: RRM (206)

(-) 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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NAB3_YEAST | P38996: 2kvi 2l41 2xnr

(-) Related Entries Specified in the PDB File

2xnr STRUCTURAL INSIGHTS INTO CIS ELEMENT RECOGNITION OF NON-POLYADENYLATED RNAS BY THE NAB3-RRM