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(-) Description

Title :  SOLUTION STRUCTURE OF THE SKELETAL MUSCLE LIM-PROTEIN 1
 
Authors :  T. N. Niraula, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  27 May 05  (Deposition) - 27 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Four And Half Lim Domains Protein 1, 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 :  T. N. Niraula, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Skeletal Muscle Lim-Protein 1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SKELETAL MUSCLE LIM-PROTEIN 1
    ChainsA
    EngineeredYES
    Expression System Plasmid040816-01
    Expression System Vector TypePLASMID
    FragmentONE AND A HALF LIM DOMAIN
    GeneFHL 1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymSLIM 1, SLIM, FOUR AND A HALF LIM DOMAINS PROTEIN 1, FHL-1

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

NMR Structure (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION

(-) Sites  (3, 3)

NMR Structure (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:8 , CYS A:11 , HIS A:30 , CYS A:33BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS A:36 , CYS A:39 , CYS A:57 , CYS A:60BINDING SITE FOR RESIDUE ZN A 401
3AC3SOFTWARECYS A:69 , CYS A:72 , HIS A:91 , CYS A:94BINDING SITE FOR RESIDUE ZN A 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

NMR Structure (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_075350C101FFHL1_HUMANUnclassified (RBMX1A)  ---AC69F
2UniProtVAR_075352C104RFHL1_HUMANUnclassified (RBMX1B)122459147AC72R
3UniProtVAR_042603W122SFHL1_HUMANDisease (SPM)122458140AW90S
4UniProtVAR_075353H123LFHL1_HUMANDisease (RBMX1A)267606812AH91L
5UniProtVAR_075354H123QFHL1_HUMANDisease (RBMX1A)267606813AH91Q
6UniProtVAR_045999H123YFHL1_HUMANDisease (RBMX1A)122458142AH91Y

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

(-) PROSITE Motifs  (2, 5)

NMR Structure (2, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIM_DOMAIN_1PS00478 LIM zinc-binding domain signature.FHL1_HUMAN40-75
101-136
162-195
  3A:8-43
A:69-95
A:100-101
2LIM_DOMAIN_2PS50023 LIM domain profile.FHL1_HUMAN99-160
38-98
161-219
  3A:67-95
A:8-66
A:100-101

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003941551bENSE00001453320X:135229680-135229787108FHL1_HUMAN-00--
1.7bENST000003941557bENSE00001029114X:135252066-13525213974FHL1_HUMAN-00--
1.10aENST0000039415510aENSE00002182486X:135288566-135288747182FHL1_HUMAN1-52521A:1-20 (gaps)37
1.11aENST0000039415511aENSE00000890595X:135289175-135289349175FHL1_HUMAN53-111591A:21-7959
1.12cENST0000039415512cENSE00000890598X:135289951-135290120170FHL1_HUMAN111-167571A:79-9820
1.13dENST0000039415513dENSE00000676980X:135290614-135290800187FHL1_HUMAN168-230631A:99-1013
1.14ENST0000039415514ENSE00000676981X:135291402-135291601200FHL1_HUMAN230-296670--
1.15cENST0000039415515cENSE00001707082X:135292030-1352935081479FHL1_HUMAN297-323270--

(-) 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:101
 aligned with FHL1_HUMAN | Q13642 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:157
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       
           FHL1_HUMAN    16 GKKYVQKDGHHCCLKCFDKFCANTCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFAKHCVKCNKAITSG 172
               SCOP domains ------------------------d2cupa3 A:8-34             d2cupa2 A:35-65                d2cupa1 A:66-95               --------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-----..------------................eeee..eeee..................eee..eeehhhhhh...................eee....eee.......---------------------------------------... Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------------------------------------------------------F--R-----------------SL------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------Q------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) -----------------------------------------------------------------------------------------------------------Y------------------------------------------------- SAPs(SNPs) (3)
                PROSITE (1) ------------------------LIM_DOMAIN_1  PDB: A:8-43           -------------------------LIM_DOMAIN_1  PDB: A:69-95          -------------------------LIM_DOMAIN_ PROSITE (1)
                PROSITE (2) ----------------------LIM_DOMAIN_2  PDB: A:8-66 UniProt: 38-98                     LIM_DOMAIN_2  PDB: A:67-95 UniProt: 99-160                    LIM_DOMAIN_2 PROSITE (2)
           Transcript 1 (1) Exon 1.10a  PDB: A:1-20 (gaps)       Exon 1.11a  PDB: A:21-79 UniProt: 53-111                   --------------------------------------------------------1.13d Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------Exon 1.12c  PDB: A:79-98 UniProt: 111-167 [INCOMPLETE]   ----- Transcript 1 (2)
                 2cup A   1 GS-----SG------------SSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFSGP---------------------------------------SSG 101
                             |     ||-         - |      13        23        33        43        53        63        73        83        93    |    -         -         -         -    |  
                             2     3|            5                                                                                           98                                      99  
                                    4                                                                                                                                                    

   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, 3)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

NMR Structure(hide GO term definitions)
Chain A   (FHL1_HUMAN | Q13642)
molecular function
    GO:0044325    ion channel binding    Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0007517    muscle organ development    The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
    GO:2000134    negative regulation of G1/S transition of mitotic cell cycle    Any cell cycle regulatory process that prevents the commitment of a cell from G1 to S phase of the mitotic cell cycle.
    GO:0010972    negative regulation of G2/M transition of mitotic cell cycle    Any cell cycle regulatory process that decreases the rate or extent of progression of a cell from G2 to M phase of the mitotic cell cycle.
    GO:0030308    negative regulation of cell growth    Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
    GO:0043268    positive regulation of potassium ion transport    Any process that activates or increases the frequency, rate or extent of the directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0003254    regulation of membrane depolarization    Any process that modulates the rate, frequency or extent of membrane depolarization. Membrane depolarization is the process in which membrane potential changes in the depolarizing direction from the resting potential, usually from negative to positive.
    GO:1901016    regulation of potassium ion transmembrane transporter activity    Any process that modulates the frequency, rate or extent of potassium ion transmembrane transporter activity.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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: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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        FHL1_HUMAN | Q136421x63 2cur 2egq

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