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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SPRPN10 VWA DOMAIN
 
Authors :  C. Riedinger, J. Boehringer, J. -F. Trempe, E. D. Lowe, N. R. Brown, K. Ge M. E. M. Noble, C. Gordon, J. A. Endicott
Date :  10 Feb 10  (Deposition) - 25 Aug 10  (Release) - 03 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Nuclear Protein, Nucleus, Ubiquitin, Proteasome (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Riedinger, J. Boehringer, J. F. Trempe, E. D. Lowe, N. R. Brown, K. Gehring, M. E. Noble, C. Gordon, J. A. Endicott
The Structure Of Rpn10 And Its Interactions With Polyubiquitin Chains And The Proteasome Subunit Rpn12.
J. Biol. Chem. V. 285 33992 2010
PubMed-ID: 20739285  |  Reference-DOI: 10.1074/JBC.M110.134510

(-) Compounds

Molecule 1 - 26S PROTEASOME REGULATORY SUBUNIT RPN10
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21D
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentVWA DOMAIN, RESIDUES 2-193
    Organism CommonFISSION YEAST
    Organism ScientificSCHIZOSACCHAROMYCES POMBE
    Organism Taxid4896
    SynonymSPRPN10

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:2 , LEU A:3 , SER A:58 , GLN A:60 , LYS A:99 , ARG A:107 , HOH A:2075 , HOH A:2265 , HOH A:2266BINDING SITE FOR RESIDUE SO4 A1194
2AC2SOFTWAREARG A:67 , ASP A:121 , GLU A:122 , HOH A:2105 , HOH A:2267 , HOH A:2268 , HOH A:2269BINDING SITE FOR RESIDUE SO4 A1195
3AC3SOFTWARELYS A:123 , ARG A:127 , ARG A:131 , HOH A:2079 , HOH A:2183 , HOH A:2270 , HOH A:2271BINDING SITE FOR RESIDUE SO4 A1196

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X5N)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ile A:22 -Pro A:23

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X5N)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VWFAPS50234 VWFA domain profile.RPN10_SCHPO5-185  1A:5-185

(-) Exons   (0, 0)

(no "Exon" information available for 2X5N)

(-) 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:189
 aligned with RPN10_SCHPO | O94444 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:192
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  
          RPN10_SCHPO     2 VLEATMILIDNSEWMINGDYIPTRFEAQKDTVHMIFNQKINDNPENMCGLMTIGDNSPQVLSTLTRDYGKFLSAMHDLPVRGNAKFGDGIQIAQLALKHRENKIQRQRIVAFVGSPIVEDEKNLIRLAKRMKKNNVAIDIIHIGELQNESALQHFIDAANSSDSCHLVSIPPSPQLLSDLVNQSPIGQGVVA 193
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---VWA_2-2x5nA01 A:5-185                                                                                                                                                                -------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eeeeee.......eeeeee.hhhhhhhhhh........hhhhhhhhhhhhhhh......eeeeeeee......hhhhhhhhhhhhhhh.eeeeeeee...---hhhhhhhhhhh.....eeeee.....hhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---VWFA  PDB: A:5-185 UniProt: 5-185                                                                                                                                                    -------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2x5n A   2 VLEATMILIDNSEWMINGDYIPTRFEAQKDTVHMIFNQKINDNPENMCGLMTIGDNSPQVLSTLTRDYGKFLSAMHDLPVRGNAKFGDGIQIAQLALKHRENKIQRQRIVAFVGSPIVEDEKNLIRLAKRMKKNNVAIDIIHIGEL---SALQHFIDAANSSDSCHLVSIPPSPQLLSDLVNQSPIGQGVVA 193
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141     | 151       161       171       181       191  
                                                                                                                                                                           147 151                                          

   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  (0, 0)

(no "SCOP Domain" information available for 2X5N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2X5N)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: vWA-like (60)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RPN10_SCHPO | O94444)
molecular function
    GO:0036435    K48-linked polyubiquitin modification-dependent protein binding    Interacting selectively and non-covalently with a protein upon poly-ubiquitination formed by linkages between lysine residues at position 48 in the target protein.
    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:0045842    positive regulation of mitotic metaphase/anaphase transition    Any process that activates or increases the frequency, rate or extent of the cell cycle process in which a cell progresses from metaphase to anaphase during mitosis, triggered by the activation of the anaphase promoting complex by Cdc20/Sleepy homolog which results in the degradation of Securin.
    GO:0043248    proteasome assembly    The aggregation, arrangement and bonding together of a mature, active proteasome complex.
    GO:0043161    proteasome-mediated 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 ubiquitin, and mediated by the proteasome.
    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: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.
    GO:0008540    proteasome regulatory particle, base subcomplex    The subcomplex of the proteasome regulatory particle that directly associates with the proteasome core complex.

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