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(-) Description

Title :  SOLUTION STRUCTURE OF THE PH DOMAIN OF KIAA0640 PROTEIN FROM HUMAN
 
Authors :  H. Li, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  25 Apr 06  (Deposition) - 25 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Ph Domain, Kiaa0640 Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Li, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Ph Domain Of Kiaa0640 Protein From Human
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KIAA0640 PROTEIN
    Chains: A
    Engineered: YES
    Expression System: CELL FREE SYNTHESIS
    Expression System Plasmid: P050919-04
    Expression System Vector Type: PLASMID
    Fragment: PH DOMAIN
    Gene: KIAA0640
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2DN6)

(-) Sites  (0, 0)

(no "Site" information available for 2DN6)

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:57 -A:76

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DN6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_059548R230GSWP70_HUMANPolymorphism397686AR27G
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.SWP70_HUMAN210-306  1A:8-103

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003189501aENSE00002163255chr11:9685624-9685825202SWP70_HUMAN1-33330--
1.2ENST000003189502ENSE00001315577chr11:9715693-9715833141SWP70_HUMAN34-80470--
1.4ENST000003189504ENSE00001103459chr11:9735013-9735186174SWP70_HUMAN81-138580--
1.6aENST000003189506aENSE00001319603chr11:9746205-9746432228SWP70_HUMAN139-214761A:1-11 (gaps)30
1.8bENST000003189508bENSE00001296150chr11:9749600-9749746147SWP70_HUMAN215-263491A:12-6049
1.9ENST000003189509ENSE00000889939chr11:9750890-9750998109SWP70_HUMAN264-300371A:61-9737
1.10ENST0000031895010ENSE00001321245chr11:9754076-9754257182SWP70_HUMAN300-360611A:97-11519
1.11bENST0000031895011bENSE00001301142chr11:9759760-9759867108SWP70_HUMAN361-396360--
1.12bENST0000031895012bENSE00000889942chr11:9761728-9761894167SWP70_HUMAN397-452560--
1.13ENST0000031895013ENSE00001319253chr11:9769405-9769603199SWP70_HUMAN452-518670--
1.14ENST0000031895014ENSE00001321762chr11:9770634-977073097SWP70_HUMAN519-551330--
1.15bENST0000031895015bENSE00001219908chr11:9771411-97745383128SWP70_HUMAN551-585350--

(-) Sequences/Alignments

NMR Structure
   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 SWP70_HUMAN | Q9UH65 from UniProtKB/Swiss-Prot  Length:585

    Alignment length:134
                                   194       204       214       224       234       244       254       264       274       284       294       304       314    
          SWP70_HUMAN   185 GQFSKGMDRQTVSMAINEVFNELILDVLKQGYMMKKGHRRKNWTERWFVLKPNIISYYVSEDLKDKKGDILLDENCCVESLPDKDGKKCLFLVKCFDKTFEISASDKKKKQEWIQAIHSTIHLLKLGSPPPHKE 318
               SCOP domains d  2dn6a                 _ A: automated matches                                                                                        SCOP domains
               CATH domains 2  dn6A0                 0 A:1-115 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--.....-----------------...eeeeeeee......eeeeeeee....eeee.......eeeee......eeeee........eeeee....eeeee...hhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------G---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------PH_DOMAIN  PDB: A:8-103 UniProt: 210-306                                                         ------------ PROSITE
           Transcript 1 (1) Exon 1.6a  PDB: A:1-11 (gaps) Exon 1.8b  PDB: A:12-60 UniProt: 215-263         ------------------------------------Exon 1.10           Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------Exon 1.9  PDB: A:61-97               ------------------ Transcript 1 (2)
                 2dn6 A   1 G--SSGSS-----------------GVLKQGYMMKKGHRRKNWTERWFVLKPNIISYYVSEDLKDKKGDILLDENCCVESLPDKDGKKCLFLVKCFDKTFEISASDKKKKQEWIQAIHSTIHLLKLGSSGPSSG 115
                            |  |   | -         -     |  11        21        31        41        51        61        71        81        91       101       111    
                            |  2   6                 7                                                                                                            
                            1
   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, 1)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DN6)

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (SWP70_HUMAN | Q9UH65)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0051017    actin filament bundle assembly    The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness.
    GO:0045190    isotype switching    The switching of activated B cells from IgM biosynthesis to biosynthesis of other isotypes of immunoglobulin, accomplished through a recombination process involving an intrachromosomal deletion involving switch regions that reside 5' of each constant region gene segment in the immunoglobulin heavy chain locus.
    GO:0030835    negative regulation of actin filament depolymerization    Any process that stops, prevents, or reduces the frequency, rate or extent of actin depolymerization.
    GO:0033633    negative regulation of cell-cell adhesion mediated by integrin    Any process that stops, prevents, or reduces the frequency, rate, or extent of cell-cell adhesion mediated by integrin.
    GO:1902309    negative regulation of peptidyl-serine dephosphorylation    Any process that stops, prevents or reduces the frequency, rate or extent of peptidyl-serine dephosphorylation.
    GO:0032233    positive regulation of actin filament bundle assembly    Any process that activates or increases the frequency, rate or extent of the assembly of actin filament bundles.
    GO:0007204    positive regulation of cytosolic calcium ion concentration    Any process that increases the concentration of calcium ions in the cytosol.
    GO:0060754    positive regulation of mast cell chemotaxis    Any process that increases the rate, frequency or extent of mast cell chemotaxis. Mast cell chemotaxis is the movement of a mast cell in response to an external stimulus.
    GO:0008064    regulation of actin polymerization or depolymerization    Any process that modulates the frequency, rate or extent of the assembly or disassembly of actin filaments by the addition or removal of actin monomers from a filament.
    GO:0032880    regulation of protein localization    Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
    GO:0016444    somatic cell DNA recombination    Recombination occurring within or between DNA molecules in somatic cells.
cellular component
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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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