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 A N-TERMINAL FRAGMENT OF SKAP-HOM CONTAINING BOTH THE HELICAL DIMERIZATION DOMAIN AND THE PH DOMAIN
 
Authors :  Y. Tang, K. D. Swanson, B. G. Neel, M. J. Eck
Date :  27 Jul 04  (Deposition) - 26 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Novel Dimerization Domain, Ph Domain, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Tang, K. D. Swanson, B. G. Neel, M. J. Eck
Structural Basis For The Dimerization And Phosphoinositide Specificity Of The Src Kinase-Associated Phosphoproteins Skap55 And Skap-Hom
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SRC-ASSOCIATED ADAPTOR PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL FRAGMENT, RESIDUES 12-222
    GeneSCAP2
    MutationYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymSKAP55 HOMOLOGUE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1U5E)

(-) Sites  (0, 0)

(no "Site" information available for 1U5E)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U5E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U5E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U5E)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.SKAP2_MOUSE116-219
 
  2A:116-219
B:116-219

(-) Exons   (0, 0)

(no "Exon" information available for 1U5E)

(-) 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:170
 aligned with SKAP2_MOUSE | Q3UND0 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:215
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217     
          SKAP2_MOUSE     8 SSPGPLPEEIRNLLADVETFVADTLKGENLSKKAKEKRESLIKKIKDVKSVYLQEFQDKGDAEDGDEYDDPFAGPADTISLASERYDKDDDGPSDGNQFPPIAAQDLPFVIKAGYLEKRRKDHSFLGFEWQKRWCALSKTVFYYYGSDKDKQQKGEFAIDGYDVRMNNTLRKDGKKDCCFEICAPDKRIYQFTAASPKDAEEWVQQLKFILQDLG 222
               SCOP domains --d    1u5ea1 A:14-222 Src-associated adaptor protein Ska                                         p2                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------1u5eA02 A:106-222 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..h----hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh-----------------------------------------....hhhhh..eeeeeeeeeeehhhhh.....eeeeeeee..eeeee.........eeee....eeee.hhhh...hhh.eeeee.....eeeee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------PH_DOMAIN  PDB: A:116-219 UniProt: 116-219                                                              --- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u5e A  12 GSP----EEIRNLLADVETFVADTLKGENLSKKAKEKRESLIKKIKDVKSVYLQEFQ-----------------------------------------FPPIAAQDLPFVIKAGYLEKRRKDHSFLGFEWQKRWCALSKTVFYYYGSDKDKQQKGEFAIDGYDVRMNNTLRKDGKKDCCFEICAPDKRIYQFTAASPKDAEEWVQQLKFILQDLG 222
                              |    |17        27        37        47        57      |  -         -         -         -       107       117       127       137       147       157       167       177       187       197       207       217     
                             14   15                                               64                                       106                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:168
 aligned with SKAP2_MOUSE | Q3UND0 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:209
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213         
          SKAP2_MOUSE    14 PEEIRNLLADVETFVADTLKGENLSKKAKEKRESLIKKIKDVKSVYLQEFQDKGDAEDGDEYDDPFAGPADTISLASERYDKDDDGPSDGNQFPPIAAQDLPFVIKAGYLEKRRKDHSFLGFEWQKRWCALSKTVFYYYGSDKDKQQKGEFAIDGYDVRMNNTLRKDGKKDCCFEICAPDKRIYQFTAASPKDAEEWVQQLKFILQDLG 222
               SCOP domains d1u5eb_ B: Src-associated adaptor protein Skap2                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------1u5eB02 B:106-222 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                         CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------PH-1u5eB01 B:117-219                                                                                   --- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------PH-1u5eB02 B:117-219                                                                                   --- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh-----------------------------------------....hhhhh......eeeeeeehhhhh.....eeeeeeee..eeeee.........eeee....eeee........hhh.eeeee.....eeeee..hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------PH_DOMAIN  PDB: B:116-219 UniProt: 116-219                                                              --- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u5e B  14 PEEIRNLLADVETFVADTLKGENLSKKAKEKRESLIKKIKDVKSVYLQEFQ-----------------------------------------FPPIAAQDLPFVIKAGYLEKRRKDHSFLGFEWQKRWCALSKTVFYYYGSDKDKQQKGEFAIDGYDVRMNNTLRKDGKKDCCFEICAPDKRIYQFTAASPKDAEEWVQQLKFILQDLG 222
                                    23        33        43        53        63|        -         -         -         -  |    113       123       133       143       153       163       173       183       193       203       213         
                                                                             64                                       106                                                                                                                    

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PH (111)
(-)
Family: PH (71)
1aPH-1u5eB01B:117-219
1bPH-1u5eB02B:117-219

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SKAP2_MOUSE | Q3UND0)
molecular function
    GO:0005070    SH3/SH2 adaptor activity    Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68).
    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).
biological process
    GO:0042113    B cell activation    The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
    GO:0002757    immune response-activating signal transduction    The cascade of processes by which a signal interacts with a receptor, causing a change in the level or activity of a second messenger or other downstream target, and ultimately leading to activation or perpetuation of an immune response.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0009967    positive regulation of signal transduction    Any process that activates or increases the frequency, rate or extent of signal transduction.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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

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 1u5e)
 
  Sites
(no "Sites" information available for 1u5e)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1u5e)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1u5e
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SKAP2_MOUSE | Q3UND0
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  SKAP2_MOUSE | Q3UND0
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SKAP2_MOUSE | Q3UND01m0v 1u5f 1u5g 2otx

(-) Related Entries Specified in the PDB File

1u5d CRYSTAL STRUCTURE OF THE PH DOMAIN OF SKAP55
1u5f CRYSTAL STRUCTURE OF THE PH DOMAIN OF SKAP-HOM WITH 8 VECTOR-DERIVED N-TERMINAL RESIDUES.
1u5g CRYSTAL STRUCTURE OF THE PH DOMAIN OF SKAP-HOM