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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST RPN14, A CHAPERONE OF THE 19S REGULATORY PARTICLE OF THE PROTEASOME
 
Authors :  S. Kim, Y. Saeki, A. Suzuki, K. Takagi, K. Fukunaga, T. Yamane, K. Kato, K T. Mizushima
Date :  08 Jan 10  (Deposition) - 16 Mar 10  (Release) - 19 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Wd40 Domain, Wd Repeat, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kim, Y. Saeki, K. Fukunaga, A. Suzuki, K. Takagi, T. Yamane, K. Tanaka, T. Mizushima, K. Kato
Crystal Structure Of Yeast Rpn14, A Chaperone Of The 19S Regulatory Particle Of The Proteasome
J. Biol. Chem. V. 285 15159 2010
PubMed-ID: 20236927  |  Reference-DOI: 10.1074/JBC.M110.104042

(-) Compounds

Molecule 1 - WD REPEAT-CONTAINING PROTEIN YGL004C
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: WD40 PROTEIN

 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 3ACP)

(-) Sites  (0, 0)

(no "Site" information available for 3ACP)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:322 -A:322

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Asn A:35 -Leu A:36
2Leu A:36 -Asn A:37
3Arg A:237 -Gln A:238
4Thr A:244 -Ser A:245
5Lys A:246 -Lys A:247
6Ser A:365 -Glu A:366

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ACP)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WD_REPEATS_1PS00678 Trp-Asp (WD) repeats signature.RPN14_YEAST193-207  1A:193-207

(-) Exons   (0, 0)

(no "Exon" information available for 3ACP)

(-) 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:417
 aligned with RPN14_YEAST | P53196 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:417
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       
          RPN14_YEAST     1 MTKTITVAHIQYDFKAVLEENDENDDEFYINVDKNLNEIKEHKIVVLGNSRGVDAGKGNTFEKVGSHLYKARLDGHDFLFNTIIRDGSKMLKRADYTAVDTAKLQMRRFILGTTEGDIKVLDSNFNLQREIDQAHVSEITKLKFFPSGEALISSSQDMQLKIWSVKDGSNPRTLIGHRATVTDIAIIDRGRNVLSASLDGTIRLWECGTGTTIHTFNRKENPHDGVNSIALFVGTDRQLHEISTSKKNNLEFGTYGKYVIAGHVSGVITVHNVFSKEQTIQLPSKFTCSCNSLTVDGNNANYIYAGYENGMLAQWDLRSPECPVGEFLINEGTPINNVYFAAGALFVSSGFDTSIKLDIISDPESERPAIEFETPTFLVSNDDEVSQFCYVSDDESNGEVLEVGKNNFCALYNLSNP 417
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...eee..hhhhhhh......eeeeeeee.....eeeeeeee......ee.....eeeeee..eeeeee..eeeeee...ee.........eeeeeeee...eeeeeee....eeeee....eeeee.......eeeeee.....eeeeee....eeeee.......eee......eeeeeee....eeeeee....eeeee....eeeeee.........eeeeeeee.......................eeeeeee....eeeee.....eeeee.......eeeeee......eeeeee...eeeeee........eeee......eeeeeee..eeeeee...eeeeeeeee......eee.....eee......eeeeeee.......eeeeee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD_REPEATS_1   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3acp A   1 MTKTITVAHIQYDFKAVLEENDENDDEFYINVDKNLNEIKEHKIVVLGNSRGVDAGKGNTFEKVGSHLYKARLDGHDFLFNTIIRDGSKMLKRADYTAVDTAKLQMRRFILGTTEGDIKVLDSNFNLQREIDQAHVSEITKLKFFPSGEALISSSQDMQLKIWSVKDGSNPRTLIGHRATVTDIAIIDRGRNVLSASLDGTIRLWECGTGTTIHTFNRKENPHDGVNSIALFVGTDRQLHEISTSKKNNLEFGTYGKYVIAGHVSGVITVHNVFSKEQTIQLPSKFTCSCNSLTVDGNNANYIYAGYENGMLAQWDLRSPECPVGEFLINEGTPINNVYFAAGALFVSSGFDTSIKLDIISDPESERPAIEFETPTFLVSNDDEVSQFCYVSDDESNGEVLEVGKNNFCALYNLSNP 417
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410
   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 3ACP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ACP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ACP)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RPN14_YEAST | P53196)
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:0070682    proteasome regulatory particle assembly    The aggregation, arrangement and bonding together of a mature, active proteasome regulatory particle complex.
    GO:0006511    ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
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: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:0000502    proteasome complex    A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.

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  Cis Peptide Bonds
    Arg A:237 - Gln A:238   [ RasMol ]  
    Asn A:35 - Leu A:36   [ RasMol ]  
    Leu A:36 - Asn A:37   [ RasMol ]  
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    Thr A:244 - Ser A:245   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        RPN14_YEAST | P53196: 3vl1

(-) Related Entries Specified in the PDB File

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