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(-) Description

Title :  SOLUTION STRUCTURE OF LIM DOMAIN IN LIM-PROTEIN 3
 
Authors :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 May 05  (Deposition) - 14 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, 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 :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of Lim Domain In Lim-Protein 3
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SKELETAL MUSCLE LIM-PROTEIN 3
    ChainsA
    EngineeredYES
    Expression System PlasmidP040830-05
    Expression System Vector TypePLASMID
    FragmentLIM DOMAIN
    GeneFHL2, DRAL, SLIM3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymSLIM 3, LIM-DOMAIN PROTEIN DRAL, FOUR AND A HALF LIM DOMAINS PROTEIN 2, FHL-2

 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: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

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X4K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X4K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X4K)

(-) PROSITE Motifs  (2, 4)

NMR Structure (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIM_DOMAIN_1PS00478 LIM zinc-binding domain signature.FHL2_HUMAN40-75
101-136
162-195
221-258
  3-
A:8-43
A:68-68
A:69-72
2LIM_DOMAIN_2PS50023 LIM domain profile.FHL2_HUMAN99-160
38-98
219-279
161-218
  3A:6-66
-
A:69-72
A:68-68

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2dENST000003933532dENSE00001515001chr2:106015508-106015299210FHL2_HUMAN-00--
1.5cENST000003933535cENSE00001776995chr2:106002997-106002818180FHL2_HUMAN1-52520--
1.7ENST000003933537ENSE00001785679chr2:105990190-105990016175FHL2_HUMAN53-111591A:1-1818
1.8ENST000003933538ENSE00001646620chr2:105984196-105984027170FHL2_HUMAN111-167571A:18-6750
1.9aENST000003933539aENSE00001788075chr2:105979928-105979742187FHL2_HUMAN168-230631A:68-72 (gaps)59
1.10eENST0000039335310eENSE00001887479chr2:105977891-105977283609FHL2_HUMAN230-279501A:72-721

(-) 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:72
 aligned with FHL2_HUMAN | Q14192 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:137
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       
           FHL2_HUMAN    94 SNEYSSKCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHAMQCVQCKKPITTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYAKKCAGCTNPISG 230
               SCOP domains -------d1x4ka2 A:8-34             d1x4ka1 A:35-66                 ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------LIM-1x4kA01 A:8-65                                        ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....................eeee..eeee.................eeee..eeeehhhhhhh...-----------.------------------------------------------------------.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LIM_D--LIM_DOMAIN_1  PDB: A:8-43           -------------------------LIM_DOMAIN_1  PDB: A:68-68        -------------------------LIM_DOMAIN PROSITE (1)
                PROSITE (2) -----LIM_DOMAIN_2  PDB: A:6-66 UniProt: 99-160                     LIM_DOMAIN_2  PDB: A:68-68 UniProt: 161-218               LIM_DOMAIN_2 PROSITE (2)
           Transcript 1 (1) Exon 1.7          ----------------------------------------------------------------------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.8  PDB: A:18-67 UniProt: 111-167 [INCOMPLETE]     Exon 1.9a  PDB: A:68-72 (gaps) UniProt: 168-230 [INCOMPLETE]    Transcript 1 (2)
                 1x4k A   1 GSSGSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHAS-----------G------------------------------------------------------PSSG  72
                                    10        20        30        40        50        60      |  -        |-         -         -         -         -         -   |   
                                                                                             67          68                                                     69   

   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 1X4K)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (27, 27)

NMR Structure(hide GO term definitions)
Chain A   (FHL2_HUMAN | Q14192)
molecular function
    GO:0050681    androgen receptor binding    Interacting selectively and non-covalently with an androgen receptor.
    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.
    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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030521    androgen receptor signaling pathway    Any series of molecular signals generated as a consequence of an androgen binding to its receptor.
    GO:0055014    atrial cardiac muscle cell development    The process whose specific outcome is the progression of an atrial cardiac muscle cell over time, from its formation to the mature state. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. The atrium is the part of the heart that receives blood into the organ.
    GO:0060347    heart trabecula formation    The process of creating a trabecula in the heart. A trabecula is a tissue element in the form of a small beam, strut or rod.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0001649    osteoblast differentiation    The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009725    response to hormone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0055015    ventricular cardiac muscle cell development    The process whose specific outcome is the progression of a ventricular cardiac muscle cell over time, from its formation to the mature state. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. The ventricle is the part of the heart that pumps blood out of the organ.
cellular component
    GO:0031430    M band    The midline of aligned thick filaments in a sarcomere; location of specific proteins that link thick filaments. Depending on muscle type the M band consists of different numbers of M lines.
    GO:0030018    Z disc    Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
    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: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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

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 Related Entries

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        FHL2_HUMAN | Q141921x4l 2d8z 2miu

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