Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF THE UBA DOMAIN IN SACCHAROMYCES CEREVISIAE PROTEIN, SWA2P
 
Authors :  N. Chim, W. E. Gall, J. Xiao, M. P. Harris, T. R. Graham, A. M. Krezel
Date :  28 May 03  (Deposition) - 23 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Uba, Ubiquitin, Swa2, Auxilin, Ubiquitin-Associated Domain, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Chim, W. E. Gall, J. Xiao, M. P. Harris, T. R. Graham, A. M. Krezel
Solution Structure Of The Ubiquitin-Binding Domain In Swa2P From Saccharomyces Cerevisiae.
Proteins: V. 54 784 2004 Struct. , Funct. , Genet.
PubMed-ID: 14997574  |  Reference-DOI: 10.1002/PROT.10636
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SWA2P
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET32-EKLIC
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UBIQUITIN-ASSOCIATED (UBA) DOMAIN
    Gene: SWA2
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: AUXILIN-LIKE PROTEIN

 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 1PGY)

(-) Sites  (0, 0)

(no "Site" information available for 1PGY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR320C1YDR320C.1IV:1108099-11060932007SWA2_YEAST1-6686681A:1-4747

(-) 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:47
 aligned with SWA2_YEAST | Q06677 from UniProtKB/Swiss-Prot  Length:668

    Alignment length:47
                                   146       156       166       176       
           SWA2_YEAST   137 ALVDEVKDMEIARLMSLGLSIEEATEFYENDVTYERYLEILKSKQKE 183
               SCOP domains d1pgya_ A: Auxilin-like protein Swa2p           SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains -Ubiq-assoc-1pgyA01 A:2-47                      Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-47 UniProt: 1-668            Transcript 1
                 1pgy A   1 ALVDEVKDMEIARLMSLGLSIEEATEFYENDVTYERYLEILKSKQKE  47
                                    10        20        30        40
   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: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1PGY)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: Ubiq-assoc] (1)

(-) Gene Ontology  (9, 9)

NMR Structure(hide GO term definitions)
Chain A   (SWA2_YEAST | Q06677)
molecular function
    GO:0030276    clathrin binding    Interacting selectively and non-covalently with a clathrin heavy or light chain, the main components of the coat of coated vesicles and coated pits, and which also occurs in synaptic vesicles.
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
biological process
    GO:0072318    clathrin coat disassembly    The disaggregation of a clathrin coat into its constituent components; results in stripping or removing the clathrin coat from clathrin-coated vesicles (CCV) before fusing with their targets. CVVs transport cargo from plasma membrane and trans-Golgi to the endosomal system.
    GO:0048309    endoplasmic reticulum inheritance    The partitioning of endoplasmic reticulum between daughter cells at cell division.
    GO:0032781    positive regulation of ATPase activity    Any process that activates or increases the rate of ATP hydrolysis by an ATPase.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1pgy)
 
  Sites
(no "Sites" information available for 1pgy)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1pgy)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1pgy
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SWA2_YEAST | Q06677
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SWA2_YEAST | Q06677
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1PGY)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1PGY)