Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  VARIABLE SMALL PROTEIN 1 OF BORRELIA TURICATAE (VSPA OR VSP1)
 
Authors :  W. R. Zueckert, B. H. Yung, A. G. Barbour, C. L. Lawson
Date :  14 Jan 05  (Deposition) - 24 Jan 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  D,E  (1x)
Keywords :  Helical Bundle, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. L. Lawson, B. H. Yung, A. G. Barbour, W. R. Zuckert
Crystal Structure Of Neurotropism-Associated Variable Surface Protein 1 (Vsp1) Of Borrelia Turicatae.
J. Bacteriol. V. 188 4522 2006
PubMed-ID: 16740958  |  Reference-DOI: 10.1128/JB.00028-06
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SURFACE PROTEIN VSPA
    Chains: A, B, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET29B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET
    Fragment: VSPA CORE RESIDUES 45-202
    Gene: VSPA
    Organism Scientific: BORRELIA TURICATAE
    Organism Taxid: 142

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDE
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   DE

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1YJG)

(-) Sites  (0, 0)

(no "Site" information available for 1YJG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YJG)

(-) Sequences/Alignments

Asymmetric 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:157
 aligned with O34000_BORTU | O34000 from UniProtKB/TrEMBL  Length:214

    Alignment length:157
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       
         O34000_BORTU    45 TKNITDAVAFAKSVKDVHTLVKSIDELAKAIGKKIGANGLETDADKNAKLISGAYSVISAVDTKLASLEKKVGISDDLKGKITTVKNASTSFLTKAKSKTADLGKDDVKDADAKTAIDIADTGAKDKGAEELIKLNTAIDALLTSAEAAVTAAINAL 201
               SCOP domains d1yjga_ A: automated matches                                                                                                                                  SCOP domains
               CATH domains 1yjgA00 A:45-201  [code=1.20.120.240, no name defined]                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..eeee....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yjg A  45 TKNITDAVAFAKSVKDVHTLVKSIDELAKAIGKKIGANGLETDADKNAKLISGAYSVISAVDTKLASLEKKVGISDDLKGKITTVKNASTSFLTKAKSKTADLGKDDVKDADAKTAIDIADTGAKDKGAEELIKLNTAIDALLTSAEAAVTAAINAL 201
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       


Chain B from PDB  Type:PROTEIN  Length:157
 aligned with O34000_BORTU | O34000 from UniProtKB/TrEMBL  Length:214

    Alignment length:157
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       
         O34000_BORTU    45 TKNITDAVAFAKSVKDVHTLVKSIDELAKAIGKKIGANGLETDADKNAKLISGAYSVISAVDTKLASLEKKVGISDDLKGKITTVKNASTSFLTKAKSKTADLGKDDVKDADAKTAIDIADTGAKDKGAEELIKLNTAIDALLTSAEAAVTAAINAL 201
               SCOP domains d1yjgb_ B: automated matches                                                                                                                                  SCOP domains
               CATH domains 1yjgB00 B:45-201  [code=1.20.120.240, no name defined]                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..eeee....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yjg B  45 TKNITDAVAFAKSVKDVHTLVKSIDELAKAIGKKIGANGLETDADKNAKLISGAYSVISAVDTKLASLEKKVGISDDLKGKITTVKNASTSFLTKAKSKTADLGKDDVKDADAKTAIDIADTGAKDKGAEELIKLNTAIDALLTSAEAAVTAAINAL 201
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       


Chain D from PDB  Type:PROTEIN  Length:155
 aligned with O34000_BORTU | O34000 from UniProtKB/TrEMBL  Length:214

    Alignment length:155
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196     
         O34000_BORTU    47 NITDAVAFAKSVKDVHTLVKSIDELAKAIGKKIGANGLETDADKNAKLISGAYSVISAVDTKLASLEKKVGISDDLKGKITTVKNASTSFLTKAKSKTADLGKDDVKDADAKTAIDIADTGAKDKGAEELIKLNTAIDALLTSAEAAVTAAINAL 201
               SCOP domains d1yjgd_ D: automated matches                                                                                                                                SCOP domains
               CATH domains 1yjgD00 D:47-201  [code=1.20.120.240, no name defined]                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeee....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yjg D  47 NITDAVAFAKSVKDVHTLVKSIDELAKAIGKKIGANGLETDADKNAKLISGAYSVISAVDTKLASLEKKVGISDDLKGKITTVKNASTSFLTKAKSKTADLGKDDVKDADAKTAIDIADTGAKDKGAEELIKLNTAIDALLTSAEAAVTAAINAL 201
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196     


Chain E from PDB  Type:PROTEIN  Length:157
 aligned with O34000_BORTU | O34000 from UniProtKB/TrEMBL  Length:214

    Alignment length:157
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       
         O34000_BORTU    45 TKNITDAVAFAKSVKDVHTLVKSIDELAKAIGKKIGANGLETDADKNAKLISGAYSVISAVDTKLASLEKKVGISDDLKGKITTVKNASTSFLTKAKSKTADLGKDDVKDADAKTAIDIADTGAKDKGAEELIKLNTAIDALLTSAEAAVTAAINAL 201
               SCOP domains d1yjge_ E: automated matches                                                                                                                                  SCOP domains
               CATH domains 1yjgE00 E:45-201  [code=1.20.120.240, no name defined]                                                                                                        CATH domains
           Pfam domains (1) Lipoprotein_6-1yjgE01 E:45-201                                                                                                                                Pfam domains (1)
           Pfam domains (2) Lipoprotein_6-1yjgE02 E:45-201                                                                                                                                Pfam domains (2)
           Pfam domains (3) Lipoprotein_6-1yjgE03 E:45-201                                                                                                                                Pfam domains (3)
           Pfam domains (4) Lipoprotein_6-1yjgE04 E:45-201                                                                                                                                Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..eeee....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yjg E  45 TKNITDAVAFAKSVKDVHTLVKSIDELAKAIGKKIGANGLETDADKNAKLISGAYSVISAVDTKLASLEKKVGISDDLKGKITTVKNASTSFLTKAKSKTADLGKDDVKDADAKTAIDIADTGAKDKGAEELIKLNTAIDALLTSAEAAVTAAINAL 201
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194
   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, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: Lipoprotein_6] (1)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,D,E   (O34000_BORTU | O34000)
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.

 Visualization

(-) Interactive Views

Asymmetric Unit
  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 1yjg)
 
  Sites
(no "Sites" information available for 1yjg)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1yjg)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 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
  1yjg
    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
  O34000_BORTU | O34000
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  O34000_BORTU | O34000
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O34000_BORTU | O34000: 2ga0

(-) Related Entries Specified in the PDB File

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