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(-) Description

Title :  C-TERMINAL RNA RECOGNITION MOTIF OF THE U11/U12 65K PROTEIN
 
Authors :  C. Netter, M. C. Wahl
Date :  11 Sep 08  (Deposition) - 09 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Rna Recognition Motif (Rrm), Rnp Motif, U11/U12-65K Protein, U11/U12 Di-Snrnp, U1A Protein, U2B Protein, Minor Spliceosomal Protein, Mrna Processing, Mrna Splicing, Nucleus, Phosphoprotein, Rna-Binding, Spliceosome, Splicing (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Netter, G. Weber, H. Benecke, M. C. Wahl
Functional Stabilization Of An Rna Recognition Motif By A Noncanonical N-Terminal Expansion
Rna V. 15 1305 2009
PubMed-ID: 19447915  |  Reference-DOI: 10.1261/RNA.1359909

(-) Compounds

Molecule 1 - RNA-BINDING PROTEIN 40
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P-1
    Expression System StrainROSETTA 2 (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Fragment65K C-TERMINAL RRM, UNP RESIDUES 380-517
    GeneU11/U12 SNRNP 65K
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRNA-BINDING MOTIF PROTEIN 40, RNA-BINDING REGION-CONTAINING PROTEIN 3, U11/U12 SMALL NUCLEAR RIBONUCLEOPROTEIN 65 KDA PROTEIN, U11/U12 SNRNP 65 KDA PROTEIN, U11/U12-65K

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3EGN)

(-) Sites  (0, 0)

(no "Site" information available for 3EGN)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EGN)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:463 -Arg A:464

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EGN)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.RBM40_HUMAN27-102
420-503
  1-
A:420-503

(-) Exons   (0, 0)

(no "Exon" information available for 3EGN)

(-) 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:120
 aligned with RBM40_HUMAN | Q96LT9 from UniProtKB/Swiss-Prot  Length:517

    Alignment length:120
                                   396       406       416       426       436       446       456       466       476       486       496       506
          RBM40_HUMAN   387 ECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARP 506
               SCOP domains d3egna_ A: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhh.hhhhhhhhhhhh.........eeeeeee....hhhhhhhhhhhhh...hhhhhhhheeeeeee...eeeeeee..hhhhhhhhhhhhh..ee..ee.eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------RRM  PDB: A:420-503 UniProt: 420-503                                                --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3egn A 387 ECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARP 506
                                   396       406       416       426       436       446       456       466       476       486       496       506

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EGN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EGN)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RBM40_HUMAN | Q96LT9)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0030626    U12 snRNA binding    Interacting selectively and non-covalently with the U12 small nuclear RNA (U12 snRNA).
    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:0097157    pre-mRNA intronic binding    Interacting selectively and non-covalently with an intronic sequence of a pre-messenger RNA (pre-mRNA).
biological process
    GO:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0032502    developmental process    A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
    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:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
cellular component
    GO:0005689    U12-type spliceosomal complex    Any spliceosomal complex that forms during the splicing of a messenger RNA primary transcript to excise an intron; the series of U12-type spliceosomal complexes is involved in the splicing of the majority of introns that contain atypical AT-AC terminal dinucleotides, as well as other non-canonical introns. The entire splice site signal, not just the terminal dinucleotides, is involved in determining which spliceosome utilizes the site.
    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.
    GO:0005681    spliceosomal complex    Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

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  Cis Peptide Bonds
    Gly A:463 - Arg A:464   [ RasMol ]  
 

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