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(-) Description

Title :  SOLUTION STRUCTURE OF THE FOURTH CH DOMAIN FROM HUMAN L-PLASTIN
 
Authors :  T. Tomizawa, T. Kigawa, S. Koshiba, M. Inoue, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  02 Dec 05  (Deposition) - 02 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  All Alpha, Calponin Homology Domain, Actin Binding, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Tomizawa, T. Kigawa, S. Koshiba, M. Inoue, S. Yokoyama
Solution Structure Of The Fourth Ch Domain From Human L-Plastin
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-PLASTIN
    ChainsA
    EngineeredYES
    Expression System PlasmidP050111-01
    Expression System Vector TypePLASMID
    FragmentCH DOMAIN
    GeneLCP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymLYMPHOCYTE CYTOSOLIC PROTEIN 1, LCP-1, LC64P

 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 2D85)

(-) Sites  (0, 0)

(no "Site" information available for 2D85)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D85)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D85)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

NMR Structure (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024398K533EPLSL_HUMANPolymorphism4941543AE24E
2UniProtVAR_030826P544APLSL_HUMANPolymorphism17067725AP35A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHPS50021 Calponin homology domain profile.PLSL_HUMAN120-236
264-375
394-503
515-624
  1-
-
-
A:8-115

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003985762ENSE00001533722chr13:46785483-4678542856PLSL_HUMAN-00--
1.3ENST000003985763ENSE00001533721chr13:46777365-46777236130PLSL_HUMAN-00--
1.5ENST000003985765ENSE00001533718chr13:46758107-4675804464PLSL_HUMAN-00--
1.6bENST000003985766bENSE00001533716chr13:46756360-46756246115PLSL_HUMAN-00--
1.8aENST000003985768aENSE00001244596chr13:46733821-4673373488PLSL_HUMAN1-22220--
1.9bENST000003985769bENSE00000923408chr13:46733124-46732961164PLSL_HUMAN22-76550--
1.10ENST0000039857610ENSE00000923407chr13:46732786-46732657130PLSL_HUMAN77-120440--
1.11ENST0000039857611ENSE00001770376chr13:46730705-46730573133PLSL_HUMAN120-164450--
1.12ENST0000039857612ENSE00001785426chr13:46729021-4672894082PLSL_HUMAN164-191280--
1.14bENST0000039857614bENSE00001651255chr13:46727080-46726915166PLSL_HUMAN192-247560--
1.15ENST0000039857615ENSE00000923403chr13:46725213-46725071143PLSL_HUMAN247-294480--
1.17ENST0000039857617ENSE00000923402chr13:46722582-4672248796PLSL_HUMAN295-326320--
1.18aENST0000039857618aENSE00000923401chr13:46721238-46721043196PLSL_HUMAN327-392660--
1.19ENST0000039857619ENSE00000923400chr13:46718655-4671857779PLSL_HUMAN392-418270--
1.20ENST0000039857620ENSE00000923399chr13:46717539-46717425115PLSL_HUMAN418-456390--
1.22ENST0000039857622ENSE00001774077chr13:46716560-46716427134PLSL_HUMAN457-501451A:1-22
1.23ENST0000039857623ENSE00000923397chr13:46708385-46708262124PLSL_HUMAN501-542421A:3-3331
1.24ENST0000039857624ENSE00000923396chr13:46705073-46704949125PLSL_HUMAN543-584421A:34-7542
1.25aENST0000039857625aENSE00001533714chr13:46701858-467000961763PLSL_HUMAN584-627441A:75-11844

(-) 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:124
 aligned with PLSL_HUMAN | P13796 from UniProtKB/Swiss-Prot  Length:627

    Alignment length:148
                                                                                                                                                                       627      
                                   495       505       515       525       535       545       555       565       575       585       595       605       615       625 |      
           PLSL_HUMAN   486 GNRTLTLALIWQLMRRYTLNILEEIGGGQKVNDDIIVNWVNETLREAKKSSSISSFKDPKISTSLPVLDLIDAIQPGSINYDLLKTENLNDDEKLNNAKYAISMARKIGARVYALPEDLVEVNPKMVMTVFACLMGKGMKRV------   -
               SCOP domains d2                        d85a_ A: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------------------------.......hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhh.....hhhhhh..hhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------E----------A----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CH  PDB: -        -----------CH  PDB: A:8-115 UniProt: 515-624                                                                             --------- PROSITE
           Transcript 1 (1) Exon 1.22       -----------------------------------------Exon 1.24  PDB: A:34-75 UniProt: 543-584  ------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.23  PDB: A:3-33 UniProt: 501-542   -----------------------------------------Exon 1.25a  PDB: A:75-118 UniProt: 584-627  ------ Transcript 1 (2)
                 2d85 A   1 GS------------------------SGSSGNDDIIVNWVNETLREAEKSSSISSFKDPKISTSLPVLDLIDAIQPGSINYDLLKTENLNDDEKLNNAKYAISMARKIGARVYALPEDLVEVNPKMVMTVFACLMGKGMKRVSGPSSG 124
                             |       -         -      |  6        16        26        36        46        56        66        76        86        96       106       116        
                             2                        3                                                                                                                         

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D85)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D85)

(-) Gene Ontology  (34, 34)

NMR Structure(hide GO term definitions)
Chain A   (PLSL_HUMAN | P13796)
molecular function
    GO:0051020    GTPase binding    Interacting selectively and non-covalently with a GTPase, any enzyme that catalyzes the hydrolysis of GTP.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0051015    actin filament binding    Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0002286    T cell activation involved in immune response    The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response.
    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:0031100    animal organ regeneration    The regrowth of a lost or destroyed animal organ.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0071803    positive regulation of podosome assembly    Any process that activates or increases the rate or extent of podosome assembly.
    GO:0010737    protein kinase A signaling    A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase A, which occurs as a result of a single trigger reaction or compound.
    GO:0033157    regulation of intracellular protein transport    Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells.
    GO:0044319    wound healing, spreading of cells    The migration of a cell along or through a wound gap that contributes to the reestablishment of a continuous surface.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005884    actin filament    A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane.
    GO:0032432    actin filament bundle    An assembly of actin filaments that 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: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: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: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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0030175    filopodium    Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination 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:0001891    phagocytic cup    An invagination of the cell membrane formed by an actin dependent process during phagocytosis. Following internalization it is converted into a phagosome.
    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.
    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.
    GO:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.
    GO:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.
    GO:0001725    stress fiber    A contractile actin filament bundle that consists of short actin filaments with alternating polarity, cross-linked by alpha-actinin and possibly other actin bundling proteins, and with myosin present in a periodic distribution along the fiber.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PLSL_HUMAN | P137965joj 5jol

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