2OTX - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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 :   09 Feb 07 (Deposition) - 27 Mar 07 (Release) - 03 Nov 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 :   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)

Molecule 1 - SRC KINASE-ASSOCIATED PHOSPHOPROTEIN 2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL FRAGMENT (RESIDUES 12-222)
	Gene	:	SKAP2, PRAP, RA70, SAPS, SCAP2, SKAP55R
	Mutation	:	YES
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	SRC FAMILY-ASSOCIATED PHOSPHOPROTEIN 2, SRC KINASE-ASSOCIATED PHOSPHOPROTEIN 55-RELATED PROTEIN, SKAP55 HOMOLOG, SKAP-HOM, SRC-ASSOCIATED ADAPTER PROTEIN WITH PH AND SH3 DOMAINS, PYK2/RAFTK-ASSOCIATED PROTEIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2OTX)

(no "SS Bond" information available for 2OTX)

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

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PH_DOMAIN	PS50003	PH domain profile.	SKAP2_MOUSE	116-219	2	A:116-219 B:116-219

(no "Exon" information available for 2OTX)

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 d2o    txa_ A: Src-associated adaptor protein Skap2                                                                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 2otx 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 d2otxb_ B: Src-associated adaptor protein Skap2                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------PH-2otxB01 B:117-219                                                                                   --- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------PH-2otxB02 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
                 2otx 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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PH domain-like barrel (258)

Superfamily: PH domain-like (257)

Family: Pleckstrin-homology domain (PH domain) (102)

Protein domain: Src-associated adaptor protein Skap2 (4)

Mouse (Mus musculus) [TaxId: 10090] (4)

1a	d2otxa_	A:
1b	d2otxb_	B:

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PH (111)

Family: PH (71)

Mus musculus (Mouse) (20)

1a	PH-2otxB01	B:117-219
1b	PH-2otxB02	B:117-219

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.

Asymmetric/Biological Unit
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	2otx
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UniProtKB/Swiss-Prot
	SKAP2_MOUSE \| Q3UND0	:	1m0v 1u5e 1u5f 1u5g

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

Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

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Gene Ontology (9, 9)

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