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(-) Description

Title :  SOLUTION STRUCTURE OF THE LIM DOMAIN OF EPITHELIAL PROTEIN LOST IN NEOPLASM
 
Authors :  X. R. Qin, T. Nagashima, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  08 Dec 05  (Deposition) - 08 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Lim Domain, Epithelial Protein Lost In Neoplasm, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. R. Qin, T. Nagashima, F. Hayashi, S. Yokoyama
Solution Structure Of The Lim Domain Of Epithelial Protein Lost In Neoplasm
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EPLIN PROTEIN
    ChainsA
    EngineeredYES
    Expression System PlasmidP050302-11
    Expression System Vector TypePLASMID
    FragmentLIM DOMAIN
    GeneEPLIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymEPITHELIAL PROTEIN LOST IN NEOPLASM

 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:39 , CYS A:42BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS A:45 , CYS A:48 , CYS A:66 , HIS A:69BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D8Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D8Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D8Y)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIM_DOMAIN_2PS50023 LIM domain profile.LIMA1_HUMAN388-448  1A:16-76
2LIM_DOMAIN_1PS00478 LIM zinc-binding domain signature.LIMA1_HUMAN390-424  1A:18-52

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003412471ENSE00001114650chr12:50677353-50677203151LIMA1_HUMAN-00--
1.2ENST000003412472ENSE00001379043chr12:50642557-50642416142LIMA1_HUMAN1-40400--
1.3ENST000003412473ENSE00000837648chr12:50625493-5062544846LIMA1_HUMAN40-55160--
1.5aENST000003412475aENSE00001060480chr12:50616268-50615804465LIMA1_HUMAN56-2101550--
1.6ENST000003412476ENSE00000424945chr12:50599851-5059976785LIMA1_HUMAN211-239290--
1.7ENST000003412477ENSE00000742546chr12:50598483-50598335149LIMA1_HUMAN239-288500--
1.8ENST000003412478ENSE00000742547chr12:50594667-50594560108LIMA1_HUMAN289-324360--
1.9ENST000003412479ENSE00000742548chr12:50589670-5058961358LIMA1_HUMAN325-344200--
1.10bENST0000034124710bENSE00000919783chr12:50586344-50586235110LIMA1_HUMAN344-380371A:1-99
1.11ENST0000034124711ENSE00000919782chr12:50575820-50575687134LIMA1_HUMAN381-425451A:10-5344
1.12bENST0000034124712bENSE00001666705chr12:50571852-505695652288LIMA1_HUMAN425-7593351A:53-91 (gaps)68

(-) 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:91
 aligned with LIMA1_HUMAN | Q9UHB6 from UniProtKB/Swiss-Prot  Length:759

    Alignment length:121
                                   381       391       401       411       421       431       441       451       461       471       481       491 
          LIMA1_HUMAN   372 ESSPPKAMKKFQAPARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGFGHRPHKDLWASKNENEEILERPAQLANARETPHSPG 492
               SCOP domains --------d 2d8ya1 A:9-43 Eplin, LIMA1        d2d8ya2 A:44-85 Eplin, LIMA1              ----------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........-....................eee....eee..................ee....eehhhhhhhhh..............-----------------------------... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------LIM_DOMAIN_2  PDB: A:16-76 UniProt: 388-448                  -------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------LIM_DOMAIN_1  PDB: A:18-52         -------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.10b    Exon 1.11  PDB: A:10-53 UniProt: 381-425     ------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.12b  PDB: A:53-91 (gaps) UniProt: 425-759 [INCOMPLETE]        Transcript 1 (2)
                 2d8y A   1 GSSGSSGMK-FQAPARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGFGSGP-----------------------------SSG  91
                                    |-|       19        29        39        49        59        69        79        |-         -         -        90 
                                    9 |                                                                            88                            89  
                                     10                                                                                                              

   Legend:   → Mismatch (orange background)
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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  (1, 2)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D8Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D8Y)

(-) Gene Ontology  (18, 18)

NMR Structure(hide GO term definitions)
Chain A   (LIMA1_HUMAN | Q9UHB6)
molecular function
    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:0003785    actin monomer binding    Interacting selectively and non-covalently with monomeric actin, also known as G-actin.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0030835    negative regulation of actin filament depolymerization    Any process that stops, prevents, or reduces the frequency, rate or extent of actin depolymerization.
    GO:0031529    ruffle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a ruffle, a projection at the leading edge of a crawling cell.
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:0005903    brush border    The dense covering of microvilli on the apical surface of a epithelial cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.
    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:0032154    cleavage furrow    The cleavage furrow is a plasma membrane invagination at the cell division site. The cleavage furrow begins as a shallow groove and eventually deepens to divide the cytoplasm.
    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: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: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: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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