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(-) Description

Title :  STRUCTURE OF SKI8P, A WD REPEAT PROTEIN INVOLVED IN MRNA DEGRADATION AND MEIOTIC RECOMBINATION
 
Authors :  A. Y. Madrona, D. K. Wilson
Date :  18 Mar 04  (Deposition) - 25 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Wd Repeat, Beta-Transducin Repeat, Wd40 Repeat, Beta Propeller, Antiviral Protein, Recombination (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Y. Madrona, D. K. Wilson
The Structure Of Ski8P, A Protein Regulating Mrna Degradation: Implications For Wd Protein Structure.
Protein Sci. V. 13 1557 2004
PubMed-ID: 15152089  |  Reference-DOI: 10.1110/PS.04704704
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTIVIRAL PROTEIN SKI8
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTYB2
    Expression System StrainBL21*
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSKI8, REC103, YGL213C
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:128 , LYS A:240 , SER A:298 , LYS A:361 , HOH A:432 , HOH A:433 , HOH A:485 , HOH A:530 , HOH A:536BINDING SITE FOR RESIDUE SO4 A 400
2AC2SOFTWAREVAL A:276 , ARG A:316 , ARG A:325 , THR A:328BINDING SITE FOR RESIDUE SO4 A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SQ9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:184 -Pro A:185

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SQ9)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WD_REPEATS_1PS00678 Trp-Asp (WD) repeats signature.SKI8_YEAST29-43
306-320
  2A:29-43
A:306-320

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGL213C1YGL213C.1VII:91251-900581194SKI8_YEAST1-3973971A:3-395 (gaps)393

(-) 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:378
 aligned with SKI8_YEAST | Q02793 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:393
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392   
           SKI8_YEAST     3 KVFIATANAGKAHDADIFSVSACNSFTVSCSGDGYLKVWDNKLLDNENPKDKSYSHFVHKSGLHHVDVLQAIERDAFELCLVATTSFSGDLLFYRITREDETKKVIFEKLDLLDSDMKKHSFWALKWGASNDRLLSHRLVATDVKGTTYIWKFHPFADESNSLTLNWSPTLELQGTVESPMTPSQFATSVDISERGLIATGFNNGTVQISELSTLRPLYNFESQHSMINNSNSIRSVKFSPQGSLLAIAHDSNSFGCITLYETEFGERIGSLSVPTHSSQASLGEFAHSSWVMSLSFNDSGETLCSAGWDGKLRFWDVKTKERITTLNMHCDDIEIEEDILAVDEHGDSLAEPGVFDVKFLKKGWRSGMGADLNESLCCVCLDRSIRWFREAG 395
               SCOP domains d1sq9a_ A: Antiviral protein Ski8 (Ski8p)                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1sq9A00 A:3-395 YVTN repeat-like/Quinoprotein amine dehydrogenase                                                                                                                                                                                                                                                                                                                                         CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-1sq9A01 A:288-319          ---------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-1sq9A02 A:288-319          ---------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-1sq9A03 A:288-319          ---------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author .eeeeeeee.......eeeeee...eeeeee...eeeeee.......hhhh.eeeee.....eeeeeeeeeee...eeeeeeeeee....eeeeeeee......eeeeee.....hhhhh.eeeeeee...----.eeeeeee....eeeeeee...hhhhhh......eeeeeeee...........eeee....eeeee....eeeeee....eeeeeee...---.....eeeeee.....eeeeeeee..eeeeeeee.....eeeee...--------........eeeeee.....eeeeee...eeeeee....eeeeeee.hhhhh.hhhhh..............eeeeeee..............eeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------WD_REPEATS_1   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD_REPEATS_1   --------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-395 (gaps) UniProt: 1-397 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                 Transcript 1
                 1sq9 A   3 KVFIATANAGKAHDADIFSVSACNSFTVSCSGDGYLKVWDNKLLDNENPKDKSYSHFVHKSGLHHVDVLQAIERDAFELCLVATTSFSGDLLFYRITREDETKKVIFEKLDLLDSDMKKHSFWALKWGASN----SHRLVATDVKGTTYIWKFHPFADESNSLTLNWSPTLELQGTVESPMTPSQFATSVDISERGLIATGFNNGTVQISELSTLRPLYNFESQH---NNSNSIRSVKFSPQGSLLAIAHDSNSFGCITLYETEFGERIGSLSVP--------GEFAHSSWVMSLSFNDSGETLCSAGWDGKLRFWDVKTKERITTLNMHCDDIEIEEDILAVDEHGDSLAEPGVFDVKFLKKGWRSGMGADLNESLCCVCLDRSIRWFREAG 395
                                    12        22        32        42        52        62        72        82        92       102       112       122       132|    | 142       152       162       172       182       192       202       212       222    |  232       242       252       262       272    |    -   |   292       302       312       322       332       342       352       362       372       382       392   
                                                                                                                                                            133  138                                                                                      227 231                                           277      286                                                                                                             

   Legend:   → Mismatch (orange background)
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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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SKI8_YEAST | Q02793)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0051321    meiotic cell cycle    Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
    GO:0070478    nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay    The chemical reactions and pathways resulting in the breakdown of the nuclear-transcribed mRNA transcript body of an mRNA in which an amino-acid codon has changed to a nonsense codon; occurs when the 3' end is not protected by a 3'-poly(A) tail; degradation proceeds in the 3' to 5' direction.
    GO:0034427    nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'    The chemical reactions and pathways resulting in the breakdown of the mRNA transcript body that occurs when the 3' end is not protected by a 3'-poly(A) tail; degradation proceeds in the 3' to 5' direction.
    GO:0070481    nuclear-transcribed mRNA catabolic process, non-stop decay    The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that is lacking a stop codon.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0065004    protein-DNA complex assembly    The aggregation, arrangement and bonding together of proteins and DNA molecules to form a protein-DNA complex.
    GO:0007131    reciprocal meiotic recombination    The cell cycle process in which double strand breaks are formed and repaired through a double Holliday junction intermediate. This results in the equal exchange of genetic material between non-sister chromatids in a pair of homologous chromosomes. These reciprocal recombinant products ensure the proper segregation of homologous chromosomes during meiosis I and create genetic diversity.
cellular component
    GO:0055087    Ski complex    A protein complex that regulates RNA degradation by the exosome complex. In Saccharomyces the complex has a heterotetrameric stoichiometry consisting of one copy each of Ski2p and Ski3 and two copies of Ski8p.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000228    nuclear chromosome    A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
    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
        SKI8_YEAST | Q027931s4u 4buj 5mc6

(-) Related Entries Specified in the PDB File

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