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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PH DOMAIN OF SKAP-HOM
 
Authors :  Y. Tang, K. Swanson, B. G. Neel, M. J. Eck
Date :  27 Jul 04  (Deposition) - 26 Jul 05  (Release) - 03 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Ph Domain, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. D. Swanson, Y. Tang, D. F. Ceccarelli, F. Poy, J. P. Sliwa, B. G. Neel, M. J. Eck
The Skap-Hom Dimerization And Ph Domains Comprise A 3'-Phosphoinositide-Gated Molecular Switch.
Mol. Cell V. 32 564 2008
PubMed-ID: 19026786  |  Reference-DOI: 10.1016/J.MOLCEL.2008.09.022
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SRC-ASSOCIATED ADAPTOR PROTEIN
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentPH DOMAIN, RESIDUES 101-222
    GeneSCAP2
    MutationYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymSKAP55 HOMOLOGUE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1U5G)

(-) Sites  (0, 0)

(no "Site" information available for 1U5G)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U5G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U5G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U5G)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.SKAP2_MOUSE116-219
 
 
 
  4A:116-219
B:116-219
C:116-219
D:116-219
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.SKAP2_MOUSE116-219
 
 
 
  1A:116-219
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.SKAP2_MOUSE116-219
 
 
 
  1-
B:116-219
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.SKAP2_MOUSE116-219
 
 
 
  1-
-
C:116-219
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.SKAP2_MOUSE116-219
 
 
 
  1-
-
-
D:116-219

(-) Exons   (0, 0)

(no "Exon" information available for 1U5G)

(-) 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:115
 aligned with SKAP2_MOUSE | Q3UND0 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:115
                                   114       124       134       144       154       164       174       184       194       204       214     
          SKAP2_MOUSE   105 QFPPIAAQDLPFVIKAGYLEKRRKDHSFLGFEWQKRWCALSKTVFYYYGSDKDKQQKGEFAIDGYDVRMNNTLRKDGKKDCCFEICAPDKRIYQFTAASPKDAEEWVQQLKFILQ 219
               SCOP domains d1u5ga1 A:105-219 Src-associated adaptor protein Skap2                                                              SCOP domains
               CATH domains -----1u5gA01 A:110-219 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeee..........eeeeeeeee..eeeee.........eeee....eeee......hhhhh.eeeee......eeee..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------PH_DOMAIN  PDB: A:116-219 UniProt: 116-219                                                               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1u5g A 105 QFPPIAAQDLPFVIKAGYLEKRRKDHSFLGFEWQKRWCALSKTVFYYYGSDKDKQQKGEFAIDGYDVRMNNTLRKDGKKDCCFEICAPDKRIYQFTAASPKDAEEWVQQLKFILQ 219
                                   114       124       134       144       154       164       174       184       194       204       214     

Chain B from PDB  Type:PROTEIN  Length:118
 aligned with SKAP2_MOUSE | Q3UND0 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:118
                                   114       124       134       144       154       164       174       184       194       204       214        
          SKAP2_MOUSE   105 QFPPIAAQDLPFVIKAGYLEKRRKDHSFLGFEWQKRWCALSKTVFYYYGSDKDKQQKGEFAIDGYDVRMNNTLRKDGKKDCCFEICAPDKRIYQFTAASPKDAEEWVQQLKFILQDLG 222
               SCOP domains d1u5gb_ B: Src-associated adaptor protein Skap2                                                                        SCOP domains
               CATH domains -----1u5gB01 B:110-222 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh..eeeeeeeeee..........eeeeeeeee..eeeee.........eeee....eeee......hhhhh.eeeee......eeee..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------PH_DOMAIN  PDB: B:116-219 UniProt: 116-219                                                              --- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1u5g B 105 QFPPIAAQDLPFVIKAGYLEKRRKDHSFLGFEWQKRWCALSKTVFYYYGSDKDKQQKGEFAIDGYDVRMNNTLRKDGKKDCCFEICAPDKRIYQFTAASPKDAEEWVQQLKFILQDLG 222
                                   114       124       134       144       154       164       174       184       194       204       214        

Chain C from PDB  Type:PROTEIN  Length:118
 aligned with SKAP2_MOUSE | Q3UND0 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:118
                                   114       124       134       144       154       164       174       184       194       204       214        
          SKAP2_MOUSE   105 QFPPIAAQDLPFVIKAGYLEKRRKDHSFLGFEWQKRWCALSKTVFYYYGSDKDKQQKGEFAIDGYDVRMNNTLRKDGKKDCCFEICAPDKRIYQFTAASPKDAEEWVQQLKFILQDLG 222
               SCOP domains d1u5gc_ C: Src-associated adaptor protein Skap2                                                                        SCOP domains
               CATH domains -----1u5gC01 C:110-222 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh..eeeeeeeeee..........eeeeeeeee..eeeee.........eeee....eeee......hhhhh.eeeee......eeee..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------PH_DOMAIN  PDB: C:116-219 UniProt: 116-219                                                              --- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1u5g C 105 QFPPIAAQDLPFVIKAGYLEKRRKDHSFLGFEWQKRWCALSKTVFYYYGSDKDKQQKGEFAIDGYDVRMNNTLRKDGKKDCCFEICAPDKRIYQFTAASPKDAEEWVQQLKFILQDLG 222
                                   114       124       134       144       154       164       174       184       194       204       214        

Chain D from PDB  Type:PROTEIN  Length:115
 aligned with SKAP2_MOUSE | Q3UND0 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:115
                                   114       124       134       144       154       164       174       184       194       204       214     
          SKAP2_MOUSE   105 QFPPIAAQDLPFVIKAGYLEKRRKDHSFLGFEWQKRWCALSKTVFYYYGSDKDKQQKGEFAIDGYDVRMNNTLRKDGKKDCCFEICAPDKRIYQFTAASPKDAEEWVQQLKFILQ 219
               SCOP domains d1u5gd_ D: Src-associated adaptor protein Skap2                                                                     SCOP domains
               CATH domains -----1u5gD01 D:110-219 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                  CATH domains
           Pfam domains (1) ------------PH-1u5gD01 D:117-219                                                                                    Pfam domains (1)
           Pfam domains (2) ------------PH-1u5gD02 D:117-219                                                                                    Pfam domains (2)
           Pfam domains (3) ------------PH-1u5gD03 D:117-219                                                                                    Pfam domains (3)
           Pfam domains (4) ------------PH-1u5gD04 D:117-219                                                                                    Pfam domains (4)
         Sec.struct. author .....hhhhh..eeeeeeeeee..........eeeeeeeee..eeeee.........eeee....eeee........hhh.eeeee......eeee..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------PH_DOMAIN  PDB: D:116-219 UniProt: 116-219                                                               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1u5g D 105 QFPPIAAQDLPFVIKAGYLEKRRKDHSFLGFEWQKRWCALSKTVFYYYGSDKDKQQKGEFAIDGYDVRMNNTLRKDGKKDCCFEICAPDKRIYQFTAASPKDAEEWVQQLKFILQ 219
                                   114       124       134       144       154       164       174       184       194       204       214     

   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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: PH (111)
(-)
Family: PH (71)
1aPH-1u5gD01D:117-219
1bPH-1u5gD02D:117-219
1cPH-1u5gD03D:117-219
1dPH-1u5gD04D:117-219

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SKAP2_MOUSE | Q3UND01m0v 1u5e 1u5f 2otx

(-) Related Entries Specified in the PDB File

1u5d CRYSTAL STRUCTURE OF THE PH DOMAIN OF SKAP55
1u5e CRYSTAL STRUCTURE OF A N-TERMINAL FRAGMENT OF SKAP-HOM CONTAINING BOTH THE HELICAL DIMERIZATION DOMAIN AND THE PH DOMAIN
1u5f CRYSTAL STRUCTURE OF THE PH DOMAIN OF SKAP-HOM WITH 8 VECTOR-DERIVED N-TERMINAL RESIDUES