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(-) Description

Title :  CRYSTAL STRUCTURE OF S.CEREVISIAE EIF6
 
Authors :  C. M. Groft, R. Beckmann, A. Sali, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  02 Nov 00  (Deposition) - 22 Nov 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Beta Barrel, Velcro Closure, Subdomain, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. M. Groft, R. Beckmann, A. Sali, S. K. Burley
Crystal Structures Of Ribosome Anti-Association Factor If6.
Nat. Struct. Biol. V. 7 1156 2000
PubMed-ID: 11101899  |  Reference-DOI: 10.1038/82017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOME ANTI-ASSOCIATION FACTOR EIF6
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System StrainBL21
    Expression System Taxid511693
    GeneTIF6
    MutationYES
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymEUKARYOTIC TRANSLATION INITIATION FACTOR 6 (EIF- 6)

 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 1G62)

(-) Sites  (0, 0)

(no "Site" information available for 1G62)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G62)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1G62)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G62)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1G62)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPR016C1YPR016C.1XVI:593066-592329738IF6_YEAST1-2452451A:1-224224

(-) 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:224
 aligned with IF6_YEAST | Q12522 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
            IF6_YEAST     1 MATRTQFENSNEIGVFSKLTNTYCLVAVGGSENFYSAFEAELGDAIPIVHTTIAGTRIIGRMTAGNRRGLLVPTQTTDQELQHLRNSLPDSVKIQRVEERLSALGNVICCNDYVALVHPDIDRETEELISDVLGVEVFRQTISGNILVGSYCSLSNQGGLVHPQTSVQDQEELSSLLQVPLVAGTVNRGSSVVGAGMVVNDYLAVTGLDTTAPELSVIESIFRL 224
               SCOP domains d1g62a_ A: Ribosome anti-association factor eIF6 (aIF6)                                                                                                                                                                          SCOP domains
               CATH domains 1g62A00 A:1-224 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......hhhhheee....eeee...hhhhhhhhhhhhh....eeee......hhhhhhee...eeeee...hhhhhhhhhhhh..............hhhhheee...eeee....hhhhhhhhhhhhh.eeee.......hhhh.eee....eee...................eee........hhhhheee....eeee...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-224 UniProt: 1-245 [INCOMPLETE]                                                                                                                                                                               Transcript 1
                 1g62 A   1 MATRTQFENSNEIGVFSKLTNTYCLVAVGGSENFYSAFEAELGDAIPIVHTTIAGTRIIGRMTAGNRRGLLVPTQTTDQELQHLRNSLPDSVKIQRVEERLSALGNVICCNDYVALVHPDIDRETEELISDVLGVEVFRQTISGNILVGSYCSLSNQGGLVHPQTSVQDQEELSSLLQVPLVAGTVNRGSSVVGAGMVVNDYLAVTGLDTTAPELSVIESIFRL 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    

   Legend:   → Mismatch (orange background)
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    → 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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G62)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IF6_YEAST | Q12522)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0043023    ribosomal large subunit binding    Interacting selectively and non-covalently with any part of the larger ribosomal subunit.
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
    GO:0003743    translation initiation factor activity    Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
    GO:1902626    assembly of large subunit precursor of preribosome    The aggregation, arrangement and bonding together of a set of components to form the large subunit precursor of the preribosome.
    GO:0000466    maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)    Any process involved in the maturation of an rRNA molecule originally produced as part of a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript.
    GO:0000463    maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)    Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule from the pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, 5.8S rRNA, and Large Subunit (LSU) in that order from 5' to 3' along the primary transcript.
    GO:0042256    mature ribosome assembly    The aggregation, arrangement and bonding together of the large and small ribosomal subunits into a functional ribosome.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0042273    ribosomal large subunit biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a large ribosomal subunit; includes transport to the sites of protein synthesis.
    GO:0000054    ribosomal subunit export from nucleus    The directed movement of a ribosomal subunit from the nucleus into the cytoplasm.
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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:0030687    preribosome, large subunit precursor    A preribosomal complex consisting of 27SA, 27SB, and/or 7S pre-rRNA, 5S rRNA, ribosomal proteins including late-associating large subunit proteins, and associated proteins; a precursor of the eukaryotic cytoplasmic large ribosomal subunit.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IF6_YEAST | Q125222x7n 3j2i 3jct 4v7f 5fl8 5h4p 5jcs 5t62

(-) Related Entries Specified in the PDB File

1g61 CRYSTAL STRUCTURE OF M.JANNASCHII IF6 TO 1.3 ANGSTROM RESOLUTION RELATED ID: NYSGXRC-P111-1 RELATED DB: TARGETDB