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 :  STRUCTURE OF A GLYCOSYLPHOSPHATIDYLINOSITOL-ANCHORED DOMAIN FROM A TRYPANOSOME VARIANT SURFACE GLYCOPROTEIN
 
Authors :  N. G. Jones, D. Nietlispach, R. Sharma, D. F. Burke, I. Eyres, M. Mues, H. R. Mott, M. Carrington
Date :  12 Oct 07  (Deposition) - 13 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (35x)
NMR Structure *:  A  (1x)
Keywords :  Membrane Protein, Immune System, Vsg Type 1 C-Terminal Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. G. Jones, D. Nietlispach, R. Sharma, D. F. Burke, I. Eyres, M. Mues, H. R. Mott, M. Carrington
Structure Of A Glycosylphosphatidylinositol-Anchored Domain From A Trypanosome Variant Surface Glycoprotein
J. Biol. Chem. V. 283 3584 2008
PubMed-ID: 18003615  |  Reference-DOI: 10.1074/JBC.M706207200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VARIANT SURFACE GLYCOPROTEIN ILTAT 1.24
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 TRXB
    Expression System Taxid: 562
    Expression System Vector: PLASMID
    Fragment: RESIDUES 445-491
    Organism Scientific: TRYPANOSOMA BRUCEI BRUCEI
    Organism Taxid: 5702
    Strain: BRUCEI
    Synonym: VSG

 Structural Features

(-) Chains, Units

  1
NMR Structure (35x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2JWH)

(-) Sites  (0, 0)

(no "Site" information available for 2JWH)

(-) SS Bonds  (2, 2)

NMR Structure
No.Residues
1A:446 -A:459
2A:454 -A:466

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JWH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2JWH)

(-) Exons   (0, 0)

(no "Exon" information available for 2JWH)

(-) 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:48
 aligned with VSI4_TRYBB | P26329 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:56
                                   445       455       465       475       485      
           VSI4_TRYBB   436 GEKNCQFNSTKASKSGVPVTQTQTAGADTTAEKCKGKGEKDCKSPDCKWEGGTCKD 491
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains ---------Trypan_glycop_C-2jwhA01 A:422-468               Pfam domains
         Sec.struct. author .--------......................................ee....ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 2jwh A 421 G--------TKASKSGVPVTQTQTAGADTTAEKCKGKGEKDCKSPDCKWEGGTCKD 468
                            |      422       432       442       452       462      
                            |      422                                              
                          421
   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 2JWH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: Trypan_glycop_C] (2)

(-) Gene Ontology  (4, 4)

NMR Structure(hide GO term definitions)
Chain A   (VSI4_TRYBB | P26329)
biological process
    GO:0020012    evasion or tolerance of host immune response    Any process, either active or passive, by which an organism avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
cellular component
    GO:0031225    anchored component of membrane    The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    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 2jwh)
 
  Sites
(no "Sites" information available for 2jwh)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2jwh)
 

(-) 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
  2jwh
    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
  VSI4_TRYBB | P26329
    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
  VSI4_TRYBB | P26329
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        VSI4_TRYBB | P26329: 2jwg 2vsg

(-) Related Entries Specified in the PDB File

1xu6 STRUCTURE OF THE C-TERMINAL DOMAIN FROM TRYPANOSOMA BRUCEI VARIANT SURFACE GLYCOPROTEIN MITAT1.2
2jwg