Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE HELICOBACTER PYLORI CAGA ONCOPROTEIN
 
Authors :  T. Hayashi, M. Senda, H. Morohashi, H. Higashi, M. Horio, Y. Kashiba, L. D. Sasaya, T. Shimizu, N. Venugopalan, H. Kumeta, N. Noda, F. Inagaki, M. Hatakeyama
Date :  23 Feb 12  (Deposition) - 25 Jul 12  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.19
Chains :  Asym./Biol. Unit :  A
Keywords :  Oncoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hayashi, M. Senda, H. Morohashi, H. Higashi, M. Horio, Y. Kashiba, L. Nagase, D. Sasaya, T. Shimizu, N. Venugopalan, H. Kumeta, N. N. Noda F. Inagaki, T. Senda, M. Hatakeyama
Tertiary Structure-Function Analysis Reveals The Pathogenic Signaling Potentiation Mechanism Of Helicobacter Pylori Oncogenic Effector Caga
Cell Host Microbe V. 12 20 2012
PubMed-ID: 22817985  |  Reference-DOI: 10.1016/J.CHOM.2012.05.010

(-) Compounds

Molecule 1 - CYTOTOXICITY-ASSOCIATED IMMUNODOMINANT ANTIGEN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 261-829
    Gene: CAGA
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: 26695
    Synonym: CAGA, CAG PATHOGENICITY ISLAND PROTEIN 26

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4DVZ)

(-) Sites  (0, 0)

(no "Site" information available for 4DVZ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DVZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DVZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DVZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DVZ)

(-) Exons   (0, 0)

(no "Exon" information available for 4DVZ)

(-) 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:459
 aligned with CAGA_HELPY | P55980 from UniProtKB/Swiss-Prot  Length:1186

    Alignment length:522
                                   317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827  
           CAGA_HELPY   308 LMGSHNGIEPEKVSLLYAGNGGFGDKHDWNATVGYKDQQGNNVATLINVHMKNGSGLVIAGGEKGINNPSFYLYKEDQLTGSQRALSQEEIRNKVDFMEFLAQNNTKLDNLSEKEKEKFQNEIEDFQKDSKAYLDALGNDRIAFVSKKDTKHSALITEFNNGDLSYTLKDYGKKADKALDREKNVTLQGSLKHDGVMFVDYSNFKYTNASKNPNKGVGATNGVSHLEAGFNKVAVFNLPDLNNLAITSFVRRNLENKLTAKGLSLQEANKLIKDFLSSNKELAGKALNFNKAVAEAKSTGNYDEVKKAQKDLEKSLRKREHLEKEVEKKLESKSGNKNKMEAKAQANSQKDEIFALINKEANRDARAIAYTQNLKGIKRELSDKLEKISKDLKDFSKSFDEFKNGKNKDFSKAEETLKALKGSVKDLGINPEWISKVENLNAALNEFKNGKNKDFSKVTQAKSDLENSVKDVIINQKVTDKVDNLNQAVSVAKAMGDFSRVEQVLADLKNFSKEQLAQQAQK 829
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee.----.eeeee.-----.....eeeeeeee.----.eeeeeeeee....eeeee.......hhhhh.eee......eee.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee.......eeeeeee....eeeeeee.----------...eeeeehhhhhheeeeee.---------------------------.eeeeee...........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....-----.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-----..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.---.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dvz A 308 LMGSHNG----KVSLLYA-----GDKHDWNATVGYKD----NVATLINVHMKNGSGLVIAGGEKGINNPSFYLYKEDQLTGSQRALSQEEIRNKVDFMEFLAQNNTKLDNLSEKEKEKFQNEIEDFQKDSKAYLDALGNDRIAFVSKKDTKHSALITEFNNGDLSYTLKDY----------EKNVTLQGSLKHDGVMFVDYS---------------------------FNKVAVFNLPDLNNLAITSFVRRNLENKLTAKGLSLQEANKLIKDFLSSNKELAGKALNFNKAVAEAKSTGNYDEVKKAQKDLEKSLRKREHLEKEVEKKLESKSGNK-----KAQANSQKDEIFALINKEANRDARAIAYTQNLKGIKRELSDKLEKISKDLKDFSKSFDEFKN-----FSKAEETLKALKGSVKDLGINPEWISKVENLNAALNEFKNG---DFSKVTQAKSDLENSVKDVIINQKVTDKVDNLNQAVSVAKAMGDFSRVEQVLADLKNFSKEQLAQQAQK 829
                                  |  - |     | -   |   337      |  - |     357       367       377       387       397       407       417       427       437       447       457       467       477|        - |     497       507 |       -         -       537       547       557       567       577       587       597       607       617       627       637      |  -  |    657       667       677       687       697       707   |   717       727       737       747       757   |   767       777       787       797       807       817       827  
                                314  319   325   331          344  349                                                                                                                              478        489                 509                         537                                                                                                        644   650                                                          711   717                                     757 761
   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 4DVZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DVZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DVZ)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CAGA_HELPY | P55980)
molecular function
    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).
    GO:0019534    toxin transporter activity    Enables the directed movement of a toxin into, out of or within a cell, or between cells. A toxin is a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.
biological process
    GO:1901998    toxin transport    The directed movement of a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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 4dvz)
 
  Sites
(no "Sites" information available for 4dvz)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4dvz)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit 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
  4dvz
    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
  CAGA_HELPY | P55980
    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
  CAGA_HELPY | P55980
    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
        CAGA_HELPY | P55980: 3iec 4dvy 4g0h 4irv

(-) Related Entries Specified in the PDB File

4dvy