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(-) Description

Title :  SOLUTION STRUCTURE OF THE LIM DOMAIN OF CARBOXYL TERMINAL LIM DOMAIN PROTEIN 1
 
Authors :  X. R. Qin, T. Nagashima, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  17 May 05  (Deposition) - 17 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Lim Domain, Pdz And Lim Domain Protein 1, Lim Domain Protein Clp-36, C-Terminal Lim Domain Protein 1, Contractile Protein, 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 Carboxyl Terminal Lim Domain Protein 1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - C-TERMINAL LIM DOMAIN PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System Plasmid: P040830-06
    Expression System Vector Type: PLASMID
    Fragment: LIM DOMAIN
    Gene: PDLIM1, CLIM1, CLP36
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL FREE PROTEIN SYNTHESIS
    Synonym: LIM DOMAIN PROTEIN CLP-36, ELFIN

 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 , ASP A:46 , 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 1X62)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X62)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X62)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIM_DOMAIN_2PS50023 LIM domain profile.PDLI1_HUMAN258-317  1A:16-73
2LIM_DOMAIN_1PS00478 LIM zinc-binding domain signature.PDLI1_HUMAN260-293  1A:18-51

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003293991aENSE00001306547chr10:97050781-97050577205PDLI1_HUMAN1-32320--
1.3ENST000003293993ENSE00000986618chr10:97031541-97031390152PDLI1_HUMAN33-83510--
1.4ENST000003293994ENSE00000986619chr10:97028619-9702853585PDLI1_HUMAN83-111290--
1.5bENST000003293995bENSE00000716582chr10:97023820-97023621200PDLI1_HUMAN112-178670--
1.6bENST000003293996bENSE00000933030chr10:97007123-97006972152PDLI1_HUMAN178-229521A:1-11
1.7cENST000003293997cENSE00000933031chr10:96998442-96998325118PDLI1_HUMAN229-268401A:1-26 (gaps)40
1.8cENST000003293998cENSE00001454795chr10:96997868-96997329540PDLI1_HUMAN268-329621A:26-7954

(-) 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:79
 aligned with PDLI1_HUMAN | O00151 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:93
                                   238       248       258       268       278       288       298       308       318   
          PDLI1_HUMAN   229 GDPNKPSGFRSVKAPVTKVAASIGNAQKLPMCDKCGTGIVGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVTPPEGY 321
               SCOP domains ---------------------d1x62a2 A:8-42                     d1x62a1 A:43-73                ------ SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------LIM-1x62A01 A:18-72                                    ------- Pfam domains
         Sec.struct. author ..----...----------........................ee....ee............hhhhhh.ee....eehhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------LIM_DOMAIN_2  PDB: A:16-73 UniProt: 258-317                 ---- PROSITE (1)
                PROSITE (2) -------------------------------LIM_DOMAIN_1  PDB: A:18-51        ---------------------------- PROSITE (2)
           Transcript 1 (1) 1--------------------------------------Exon 1.8c  PDB: A:26-79 UniProt: 268-329 [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) Exon 1.7c  PDB: A:1-26 (gaps)           ----------------------------------------------------- Transcript 1 (2)
                 1x62 A   1 GS----SGS----------SGSIGNAQKLPMCDKCGTGIVGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPSSG  79
                             |    | |-         6        16        26        36        46        56        66        76   
                             2    3 5          6
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  - → 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
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X62)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: LIM] (23)

(-) Gene Ontology  (10, 10)

NMR Structure(hide GO term definitions)
Chain A   (PDLI1_HUMAN | O00151)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0001666    response to hypoxia    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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0006979    response to oxidative stress    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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
    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:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

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 Related Entries

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        PDLI1_HUMAN | O00151: 2pkt

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