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(-) Description

Title :  SOLUTION STRUCTURE OF RNA BINDING DOMAIN IN EUKARYOTIC TRANSLATION INITIATION FACTOR 4H
 
Authors :  K. Tsuda, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  26 Apr 06  (Deposition) - 26 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Rrm Domain, Rbd, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tsuda, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 4H
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EUKARYOTIC TRANSLATION INITIATION FACTOR 4H
    Chains: A
    Engineered: YES
    Expression System: CELL FREE SYNTHESIS
    Expression System Plasmid: P050627-12
    Expression System Vector Type: PLASMID
    Fragment: RNA RECOGNITION MOTIF
    Gene: WBSCR1, EIF4H
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: EIF-4H, WILLIAMS-BEUREN SYNDROME CHROMOSOME REGION 1 PROTEIN HOMOLOG

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2DNG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Pro A:39 -Pro A:40

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.IF4H_MOUSE42-118  1A:41-117

(-) Exons   (0, 0)

(no "Exon" information available for 2DNG)

(-) 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:103
 aligned with IF4H_MOUSE | Q9WUK2 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:138
                                    29        39        49        59        69        79        89        99       109       119       129       139       149        
           IF4H_MOUSE    20 GSRGSAGGHGSRSQKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQDKGGFGFRKGGPDDRGMGGSRESRGGWDSRDDFNSG 157
               SCOP domains d2dnga_        A: automated matches                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......-------........eeeeee......hhhhhhhhh....eeeeeeee......eeeeeeeee.hhhhhhhhhhhh..ee..ee.eeee.........-------..---------------------... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------RRM  PDB: A:41-117 UniProt: 42-118                                           --------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dng A  26 GSSGSSG-------KELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQDKS-------GP---------------------SSG 128
                                  |  -    |   38        48        58        68        78        88        98       108       118    |    -  ||     -         -     |  
                                 32      33                                                                                       123     124|                   126  
                                                                                                                                           125
   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (IF4H_MOUSE | Q9WUK2)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0033592    RNA strand annealing activity    Facilitates the base-pairing of complementary single-stranded RNA.
    GO:0034057    RNA strand-exchange activity    Facilitates the displacement of one strand of an RNA-RNA duplex and its replacement with a different strand of higher complementarity.
    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:0043024    ribosomal small subunit binding    Interacting selectively and non-covalently with any part of the small ribosomal subunit.
    GO:0003743    translation initiation factor activity    Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
    GO:0002181    cytoplasmic translation    The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein.
    GO:0048589    developmental growth    The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another.
    GO:0097010    eukaryotic translation initiation factor 4F complex assembly    The aggregation, arrangement and bonding together of a set of components to form the eukaryotic translation initiation factor 4F complex.
    GO:0001731    formation of translation preinitiation complex    The joining of the small ribosomal subunit, ternary complex, and mRNA.
    GO:0019953    sexual reproduction    A reproduction process that creates a new organism by combining the genetic material of two organisms. It occurs both in eukaryotes and prokaryotes: in multicellular eukaryotic organisms, an individual is created anew; in prokaryotes, the initial cell has additional or transformed genetic material. In a process called genetic recombination, genetic material (DNA) originating from two different individuals (parents) join up so that homologous sequences are aligned with each other, and this is followed by exchange of genetic information. After the new recombinant chromosome is formed, it is passed on to progeny.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006413    translational initiation    The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016281    eukaryotic translation initiation factor 4F complex    The eukaryotic translation initiation factor 4F complex is composed of eIF4E, eIF4A and eIF4G; it is involved in the recognition of the mRNA cap, ATP-dependent unwinding of the 5'-terminal secondary structure and recruitment of the mRNA to the ribosome.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0005844    polysome    A multiribosomal structure representing a linear array of ribosomes held together by messenger RNA. They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro.

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