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(-) Description

Title :  SOLUTION STRUCTURE OF YEAST PRP24-RRM2 BOUND TO A FRAGMENT OF U6 RNA
 
Authors :  S. A. Martin-Tumasz, S. E. Butcher
Date :  27 Mar 09  (Deposition) - 09 Mar 10  (Release) - 14 Apr 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (10x)
Keywords :  Protein/Rna, Rrm, Snrnp, Splicing, Mrna Processing, Mrna Splicing, Nucleus, Phosphoprotein, Rna-Binding, Splicing- Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Martin-Tumasz, N. J. Reiter, D. A. Brow, S. E. Butcher
Structure And Functional Implications Of A Complex Containing A Segment Of U6 Rna Bound By A Domain Of Prp24.
Rna V. 16 792 2010
PubMed-ID: 20181740  |  Reference-DOI: 10.1261/RNA.1913310

(-) Compounds

Molecule 1 - U4/U6 SNRNA-ASSOCIATED-SPLICING FACTOR PRP24
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 115-197
    Gene: PRP24, YMR268C, YM8156.10C
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: U4/U6 SNRNP PROTEIN
 
Molecule 2 - 5'-R(*AP*GP*AP*GP*AP*U)-3'
    Chains: B
    Engineered: YES
    Other Details: SYNTHETIC RNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (10x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2KH9)

(-) Sites  (0, 0)

(no "Site" information available for 2KH9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2KH9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2KH9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KH9)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.PRP24_YEAST41-116
117-195
210-289		  1-
A:117-195
-

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YMR268C1YMR268C.1XIII:804221-8028871335PRP24_YEAST1-4444441A:114-199 (gaps)95

(-) 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)
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:86
 aligned with PRP24_YEAST | P49960 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:95
                                   123       133       143       153       163       173       183       193       203     
          PRP24_YEAST   114 LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLE 208
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----RRM_1-2kh9A01 A:119-189                                                ------------------- Pfam domains
         Sec.struct. author ....eeeee......hhhhhhhhhhhh...eeeee............eeeee..hhhhhhhhhhhh..ee..ee.eeee.....---------.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RRMRRM  PDB: A:117-195 UniProt: 117-195                                           ------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:114-199 (gaps) UniProt: 1-444 [INCOMPLETE]                                     Transcript 1
                 2kh9 A 114 MTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLE---------LE 199
                                   123       133       143       153       163       173       183       193   |     -   | 
                                                                                                             197       198 


Chain B from PDB  Type:RNA  Length:6
                                      
                 2kh9 B  49 AGAGAU  54
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 2KH9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2KH9)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: RRM (206)

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (PRP24_YEAST | P49960)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0017070    U6 snRNA binding    Interacting selectively and non-covalently with the U6 small nuclear RNA (U6 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: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:0017069    snRNA binding    Interacting selectively and non-covalently with a small nuclear RNA (snRNA).
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: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:0000245    spliceosomal complex assembly    The aggregation, arrangement and bonding together of a spliceosomal complex, a ribonucleoprotein apparatus that catalyzes nuclear mRNA splicing via transesterification reactions.
    GO:0000244    spliceosomal tri-snRNP complex assembly    The formation of a tri-snRNP complex containing U4 and U6 (or U4atac and U6atac) snRNAs and U5 snRNAs and associated proteins. This includes reannealing of U4 and U6 (or U4atac and U6atac) snRNAs released from previous rounds of splicing to reform the U4/U6 snRNP (or U4atac/U6atac snRNP) as well as the subsequent association of the U5 snRNP with the U4/U6 snRNP (or U4atac/U6atac snRNP) to form a tri-snRNP that is ready to reassemble into another spliceosome complex.
cellular component
    GO:0005688    U6 snRNP    A ribonucleoprotein complex that contains small nuclear RNA U6.
    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
        PRP24_YEAST | P49960: 2ghp 2go9 2l9w 4n0t 5tf6

(-) Related Entries Specified in the PDB File

7070