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(-) Description

Title :  A DUAL MODE OF RNA RECOGNITION BY THE RBMY PROTEIN
 
Authors :  L. Skrisovska, C. Bourgois, R. Stefl, L. Kister, P. Wenter, D. Elliot, J. Stevenin, F. H. T. Allain
Date :  07 Feb 06  (Deposition) - 06 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (17x)
Keywords :  Rna Binding Protein, Structure, Protein-Rna Complex, Rna Stem-Loop, Structural Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Skrisovska, C. Bourgois, R. Stefl, L. Kister, P. Wenter, D. Elliot, J. Stevenin, F. H. T. Allain
The Testis-Specific Human Protein Rbmy Recognizes Rna Through A Novel Mode Of Interaction
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA-BINDING MOTIF PROTEIN, Y CHROMOSOME, FAMILY 1 MEMBER A1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 1-116
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RNA-BINDING MOTIF PROTEIN 1, RRM, RBMY
 
Molecule 2 - S1A STEM-LOOP RNA
    Chains: B
    Engineered: YES
    Other Details: THIS SEQUENCE WAS FOUND BY IN VITRO SELEX
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (17x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2FY1)

(-) Sites  (0, 0)

(no "Site" information available for 2FY1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FY1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FY1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FY1)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.RBY1A_HUMAN8-85  1A:8-85
RBY1C_HUMAN8-85  1A:8-85

(-) Exons   (0, 0)

(no "Exon" information available for 2FY1)

(-) 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:108
 aligned with RBY1A_HUMAN | P0DJD3 from UniProtKB/Swiss-Prot  Length:496

    Alignment length:108
                                    10        20        30        40        50        60        70        80        90       100        
          RBY1A_HUMAN     1 MVEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGS 108
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeee......hhhhhhhhhhh.....eeeee.........eeeee..hhhhhhhhhhhh..........eeee.......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -------RRM  PDB: A:8-85 UniProt: 8-85                                                ----------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2fy1 A   1 MVEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGS 108
                                    10        20        30        40        50        60        70        80        90       100        


Chain A from PDB  Type:PROTEIN  Length:108
 aligned with RBY1C_HUMAN | P0DJD4 from UniProtKB/Swiss-Prot  Length:496

    Alignment length:108
                                    10        20        30        40        50        60        70        80        90       100        
          RBY1C_HUMAN     1 MVEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAQKPSFQSGGRRRPPASSRNRSPSGS 108
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeee......hhhhhhhhhhh.....eeeee.........eeeee..hhhhhhhhhhhh..........eeee.......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------RRM  PDB: A:8-85 UniProt: 8-85                                                ----------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2fy1 A   1 MVEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGS 108
                                    10        20        30        40        50        60        70        80        90       100        


Chain B from PDB  Type:RNA  Length:21
                                                     
                 2fy1 B 109 GGACUGUCCACAAGACAGUCC 129
                                   118       128
   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)

(no "SCOP Domain" information available for 2FY1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FY1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FY1)

(-) Gene Ontology  (9, 15)

NMR Structure(hide GO term definitions)
Chain A   (RBY1C_HUMAN | P0DJD4)
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.
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.
cellular component
    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.

Chain A   (RBY1A_HUMAN | P0DJD3)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    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).
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:0000381    regulation of alternative mRNA splicing, via spliceosome    Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs.
cellular component
    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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