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(-) Description

Title :  SOLUTION STRUCTURE OF THE LIM DOMAIN OF HUMAN LEUPAXIN
 
Authors :  M. Yoneyama, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  09 May 05  (Deposition) - 09 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Leupaxin, Paxillin Family, Protein-Protein Interaction, Lim Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Yoneyama, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Lim Domain Of Human Leupaxin
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LEUPAXIN
    ChainsA
    EngineeredYES
    Expression System PlasmidP040809-04
    Expression System Vector TypePLASMID
    FragmentLIM DOMAIN
    GeneLPXN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:18 , CYS A:21 , HIS A:38 , CYS A:41BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS A:44 , CYS A:47 , CYS A:65 , HIS A:68BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X3H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X3H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X3H)

(-) PROSITE Motifs  (2, 4)

NMR Structure (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIM_DOMAIN_2PS50023 LIM domain profile.LPXN_HUMAN150-209
268-327
210-267
328-386
  3-
A:16-73
A:4-15
A:74-80
2LIM_DOMAIN_1PS00478 LIM zinc-binding domain signature.LPXN_HUMAN152-185
211-244
270-303
329-362
  2-
-
A:18-51
A:74-80

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2cENST000003950742cENSE00002146350chr11:58343334-58343233102LPXN_HUMAN1-550--
1.4bENST000003950744bENSE00001322592chr11:58338186-58338029158LPXN_HUMAN5-57530--
1.5ENST000003950745ENSE00000718929chr11:58331674-5833162847LPXN_HUMAN58-73160--
1.6aENST000003950746aENSE00000851340chr11:58322413-58322314100LPXN_HUMAN73-106340--
1.8ENST000003950748ENSE00001173996chr11:58318705-58318538168LPXN_HUMAN107-162560--
1.9ENST000003950749ENSE00000718909chr11:58317619-58317446174LPXN_HUMAN163-220581A:1-33
1.10ENST0000039507410ENSE00000718901chr11:58317340-5831725982LPXN_HUMAN221-248281A:4-74
1.11ENST0000039507411ENSE00000718895chr11:58295664-58295516149LPXN_HUMAN248-297501A:7-45 (gaps)50
1.12cENST0000039507412cENSE00002140275chr11:58295196-58294344853LPXN_HUMAN298-386891A:46-80 (gaps)41

(-) 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:80
 aligned with LPXN_HUMAN | O60711 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:153
                                   195       205       215       225       235       245       255       265       275       285       295       305       315       325       335   
           LPXN_HUMAN   186 GSSPFFERSGLAYCPNDYHQLFSPRCAYCAAPILDKVLTAMNQTWHPEHFFCSHCGEVFGAEGFHEKDKKPYCRKDFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRGTLCHGCGQPITG 338
               SCOP domains --------------------------------------------------------------------------d1x3ha1 A:8-42 Leupaxin            d1x3ha2 A:43-74 Leupaxin             ------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------LIM-1x3hA01 A:18-73                                     ------------- Pfam domains
         Sec.struct. author ...--------------------------------------------------------....-----------......................eee..eee...................ee....eehhhhhhhhh-----h..-.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LIM_DOMAIN_2  PDB: -    LIM_DOMAIN_2  PDB: A:4-15 UniProt: 210-267                LIM_DOMAIN_2  PDB: A:16-73 UniProt: 268-327                 LIM_DOMAIN_ PROSITE (1)
                PROSITE (2) -------------------------LIM_DOMAIN_1  PDB: -              -------------------------LIM_DOMAIN_1  PDB: A:18-51        -------------------------LIM_DOMAIN PROSITE (2)
           Transcript 1 (1) Exon 1.9  PDB: A:1-3 [INCOMPLETE]  Exon 1.10  PDB: A:4-7       -------------------------------------------------Exon 1.12c  PDB: A:46-80 (gaps)           Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------Exon 1.11  PDB: A:7-45 (gaps) UniProt: 248-297    ----------------------------------------- Transcript 1 (2)
                 1x3h A   1 GSS--------------------------------------------------------GSSG-----------KDFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRR-----GSG-PSSG  80
                              |      -         -         -         -         -         4  |      -    |   13        23        33        43        53        63        73     | |77   
                              3                                                        4  7           8                                                               73    74 | |   
                                                                                                                                                                              76 |   
                                                                                                                                                                                77   

   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, 2)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X3H)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (21, 21)

NMR Structure(hide GO term definitions)
Chain A   (LPXN_HUMAN | O60711)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
    GO:0003712    transcription cofactor activity    Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0050859    negative regulation of B cell receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a B cell.
    GO:0007162    negative regulation of cell adhesion    Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0033628    regulation of cell adhesion mediated by integrin    Any process that modulates the frequency, rate, or extent of cell adhesion mediated by integrin.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LPXN_HUMAN | O607114xef 4xek 4xev

(-) Related Entries Specified in the PDB File

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