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(-) Description

Title :  SOLUTION STRUCTURE OF THE PH DOMAIN OF KINDLIN-3 FROM HUMAN
 
Authors :  H. Li, M. Sato, S. Koshiba, S. Watanabe, T. Harada, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  03 Apr 07  (Deposition) - 09 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Ph Domain, Unc-112-Related Protein 2, Kindlin-3, 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, M. Sato, S. Koshiba, S. Watanabe, T. Harada, T. Kigawa, S. Yokoyama
Solution Structure Of The Ph Domain Of Kindlin-3 From Human
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNC-112-RELATED PROTEIN 2
    ChainsA
    EngineeredYES
    Expression System PlasmidP060904-05
    Expression System Vector TypePLASMID
    FragmentPH DOMAIN, UNP RESIDUES 349-478
    GeneURP2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymKINDLIN-3, MIG2-LIKE

 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 2YS3)

(-) Sites  (0, 0)

(no "Site" information available for 2YS3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YS3)

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Ala A:49 -Pro A:50

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YS3)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.URP2_HUMAN354-457  1A:13-112

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002792271ENSE00001295933chr11:63974152-63974286135URP2_HUMAN-00--
1.2ENST000002792272ENSE00001314629chr11:63974823-63974996174URP2_HUMAN1-54540--
1.3ENST000002792273ENSE00001307532chr11:63978083-63978316234URP2_HUMAN54-132790--
1.4ENST000002792274ENSE00001310322chr11:63978524-63978643120URP2_HUMAN132-172410--
1.5ENST000002792275ENSE00001298304chr11:63978747-63978915169URP2_HUMAN172-228570--
1.6ENST000002792276ENSE00001316856chr11:63979117-63979219103URP2_HUMAN228-262350--
1.7ENST000002792277ENSE00001290153chr11:63986723-63986830108URP2_HUMAN263-298360--
1.8ENST000002792278ENSE00001312768chr11:63986996-63987130135URP2_HUMAN299-343451A:1-55
1.9ENST000002792279ENSE00001300977chr11:63987212-6398726150URP2_HUMAN344-360171A:6-1813
1.10aENST0000027922710aENSE00001299282chr11:63987351-63987487137URP2_HUMAN360-406471A:19-6143
1.11ENST0000027922711ENSE00001316408chr11:63987692-63987798107URP2_HUMAN406-441361A:61-9636
1.12ENST0000027922712ENSE00000992451chr11:63987908-63988141234URP2_HUMAN442-519781A:97-13741
1.13ENST0000027922713ENSE00000992452chr11:63988488-63988612125URP2_HUMAN520-561420--
1.14ENST0000027922714ENSE00000992453chr11:63990520-63990661142URP2_HUMAN561-608480--
1.15ENST0000027922715ENSE00001389860chr11:63990785-63991363579URP2_HUMAN609-667590--

(-) 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:137
 aligned with URP2_HUMAN | Q86UX7 from UniProtKB/Swiss-Prot  Length:667

    Alignment length:147
                                   345       355       365       375       385       395       405       415       425       435       445       455       465       475       
           URP2_HUMAN   336 GSAPTDVLDSLTTIPELKDHLRIFRIPRRPRKLTLKGYRQHWVVFKETTLSYYKSQDEAPGDPIQQLNLKGCEVVPDVNVSGQKFCIKLLVPSPEGMSEIYLRCQDEQQYARWMAGCRLASKGRTMADSSYTSEVQAILAFLSLQRT 482
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------PH-----2ys3A01 A:17-112                                                                             ------------------------- Pfam domains (1)
           Pfam domains (2) -------------FERM_M-2ys3----A02 A:8-133                                                                                                        ---- Pfam domains (2)
         Sec.struct. author .....------....eee...ee.----.............eeeee..eeeee...........eee.....eeee........eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------PH_DOMAIN  PDB: A:13-112 UniProt: 354-457                                                               ------------------------- PROSITE
           Transcript 1 (1) Exon 1.8----------------Exon 1.10a  PDB: A:19-61 UniProt: 360-406      -----------------------------------Exon 1.12  PDB: A:97-137 UniProt: 442-519 Transcript 1 (1)
           Transcript 1 (2) --------Exon 1.9         ---------------------------------------------Exon 1.11  PDB: A:61-96             ----------------------------------------- Transcript 1 (2)
                 2ys3 A   1 GSSGS------SGIPELKDHLRIF----RPRKLTLKGYRQHWVVFKETTLSYYKSQDEAPGDPIQQLNLKGCEVVPDVNVSGQKFCIKLLVPSPEGMSEIYLRCQDEQQYARWMAGCRLASKGRTMADSSYTSEVQAILAFLSLQRT 137
                                |    - |      14   |    20        30        40        50        60        70        80        90       100       110       120       130       
                                5      6          18   19                                                                                                                      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 2YS3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YS3)

(-) Pfam Domains  (2, 2)

NMR Structure
(-)
Clan: PH (111)
(-)
Family: PH (71)

(-) Gene Ontology  (14, 14)

NMR Structure(hide GO term definitions)
Chain A   (URP2_HUMAN | Q86UX7)
molecular function
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0033622    integrin activation    The aggregation, arrangement and bonding together of an integrin, a heterodimeric adhesion receptor formed by the non-covalent association of particular alpha and beta subunits, that lead to the increased affinity of the integrin for its extracellular ligands.
    GO:0007229    integrin-mediated signaling pathway    A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0007159    leukocyte cell-cell adhesion    The attachment of a leukocyte to another cell via adhesion molecules.
    GO:0070527    platelet aggregation    The adhesion of one platelet to one or more other platelets via adhesion molecules.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0033632    regulation of cell-cell adhesion mediated by integrin    Any process that modulates the frequency, rate, or extent of cell-cell adhesion mediated by integrin.
    GO:0034446    substrate adhesion-dependent cell spreading    The morphogenetic process that results in flattening of a cell as a consequence of its adhesion to a substrate.
cellular component
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0002102    podosome    An actin-rich adhesion structure characterized by formation upon cell substrate contact and localization at the substrate-attached part of the cell, contain an F-actin-rich core surrounded by a ring structure containing proteins such as vinculin and talin, and have a diameter of 0.5 mm.

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    Ala A:49 - Pro A:50   [ RasMol ]  
 

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