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(-) Description

Title :  NMR STRUCTURE OF THE RNA BINDING DOMAIN OF HUMAN FOX-1 IN COMPLEX WITH UGCAUGU
 
Authors :  F. H. Allain, S. D. Auweter
Date :  25 Oct 05  (Deposition) - 10 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (30x)
Keywords :  Protein-Rna Complex, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. D. Auweter, R. Fasan, L. Reymond, J. G. Underwood, D. L. Black, S. Pitsch, F. H. Allain
Molecular Basis Of Rna Recognition By The Human Alternative Splicing Factor Fox-1.
Embo J. V. 25 163 2006
PubMed-ID: 16362037  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600918
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ATAXIN-2-BINDING PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A+
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RNA BINDING DOMAIN
    Gene: A2BP1, A2BP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - UGCAUGU
    Chains: B
    Engineered: YES
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (30x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2ERR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 32)

NMR Structure
No.ModelResidues
11, 5, 6, 7, 8, 9, 10, 12, 13, 15, 17, 18, 19, 20, 21, 24, 26, 27, 28, 30Ala A:193 -Arg A:194
22, 8, 9, 15, 24, 25, 26, 30Lys A:117 -Arg A:118
321, 29Gln A:115 -Pro A:116
421, 24Val A:195 -Met A:196

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.RFOX1_HUMAN117-193  1A:117-193

(-) Exons   (0, 0)

(no "Exon" information available for 2ERR)

(-) 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:88
 aligned with RFOX1_HUMAN | Q9NWB1 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:88
                                   118       128       138       148       158       168       178       188        
          RFOX1_HUMAN   109 NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVM 196
               SCOP domains d2erra1 A:109-196 Ataxin-2-binding protein 1                                             SCOP domains
               CATH domains -----2errA01 A:114-196  [code=3.30.70.330, no name defined]                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee......hhhhhhhhhhhh.....eee.........eeeee...hhhhhhhhhhhh..ee..ee.eeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------RRM  PDB: A:117-193 UniProt: 117-193                                         --- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 2err A 109 NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVM 196
                                   118       128       138       148       158       168       178       188        


Chain B from PDB  Type:RNA  Length:7
                                       
                 2err B 197 UGCAUGU 203
   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  (1, 1)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A   (RFOX1_HUMAN | Q9NWB1)
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:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0050658    RNA transport    The directed movement of RNA, ribonucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0043484    regulation of RNA splicing    Any process that modulates the frequency, rate or extent of 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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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  Cis Peptide Bonds
    Ala A:193 - Arg A:194   [ RasMol ]  
    Gln A:115 - Pro A:116   [ RasMol ]  
    Lys A:117 - Arg A:118   [ RasMol ]  
    Val A:195 - Met A:196   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        RFOX1_HUMAN | Q9NWB1: 2n82 4zka

(-) Related Entries Specified in the PDB File

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