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

(-) Description

Title :  STRUCTURE OF AT3G01050, A UBIQUITIN-FOLD PROTEIN FROM ARABIDOPSIS THALIANA
 
Authors :  B. F. Volkman, B. L. Lytle, F. C. Peterson, Center For Eukaryotic Structural Genomics (Cesg)
Date :  16 Feb 04  (Deposition) - 24 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Ubiquitin-Like, Cell-Free, Wheat Germ, Structural Genomics, Protein Structure Initiative, Cesg, Psi, Center For Eukaryotic Structural Genomics, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. Vinarov, B. L. Lytle, F. C. Peterson, E. M. Tyler, B. F. Volkman, J. L. Markley
Cell-Free Protein Production And Labeling Protocol For Nmr-Based Structural Proteomics.
Nat. Methods V. 1 149 2004
PubMed-ID: 15782178  |  Reference-DOI: 10.1038/NMETH716
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN FAMILY
    Chains: A
    Engineered: YES
    Expression System: CELL-FREE SYNTHESIS
    Expression System Plasmid: PEU-AT3G01050
    Expression System Vector Type: PLASMID
    Gene: AT3G01050
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: AT3G01050
    Other Details - Source: WHEAT GERM CELL-FREE, IN VITRO EXPRESSION

 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 1SE9)

(-) Sites  (0, 0)

(no "Site" information available for 1SE9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SE9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SE9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SE9)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.MUB1_ARATH8-74  1A:8-74

(-) Exons   (0, 0)

(no "Exon" information available for 1SE9)

(-) 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:101
 aligned with MUB1_ARATH | Q9MAB9 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:101
                                    10        20        30        40        50        60        70        80        90       100 
           MUB1_ARATH     1 MAEVHNQLEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAVTTMHVIIQAPVTEKEK 101
               SCOP domains d1se9a_ A: Hypothetical protein At3g01050                                                             SCOP domains
               CATH domains 1se9A00 A:1-101 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1                    CATH domains
               Pfam domains -----Rad60-SLD_2-1se9A01 A:6-101                                                                      Pfam domains
         Sec.struct. author .......eeeeeee....eeeeeee....hhhhhhhhhhhhh.........hhh.eeeee..ee.....hhhhhh..........eeeeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------UBIQUITIN_2  PDB: A:8-74 UniProt: 8-74                             --------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 1se9 A   1 EAEVHNQLEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAVTTMHVIIQAPVTEKEK 101
                                    10        20        30        40        50        60        70        80        90       100
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (3, 3)

NMR Structure(hide GO term definitions)
Chain A   (MUB1_ARATH | Q9MAB9)
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.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 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 1se9)
 
  Sites
(no "Sites" information available for 1se9)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1se9)
 

(-) 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
  1se9
    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
  MUB1_ARATH | Q9MAB9
    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
  MUB1_ARATH | Q9MAB9
    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 1SE9)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1SE9)