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(-) Description

Title :  1ST LIM DOMAIN OF PINCH PROTEIN
 
Authors :  A. Velyvis, Y. Yang, C. Wu, J. Qin
Date :  26 Oct 00  (Deposition) - 21 Feb 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (25x)
Keywords :  Lim Domain; Zn Finger, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Velyvis, Y. Yang, C. Wu, J. Qin
Solution Structure Of The Focal Adhesion Adaptor Pinch Lim1 Domain And Characterization Of Its Interaction With The Integrin-Linked Kinase Ankyrin Repeat Domain.
J. Biol. Chem. V. 276 4932 2001
PubMed-ID: 11078733  |  Reference-DOI: 10.1074/JBC.M007632200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PINCH PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMAL-C2X
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: LIM1 DOMAIN, RESIDUES 1-70
    Gene: LIMS1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PARTICULARLY INTERESTING NEW CYS-HIS PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (25x): 

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:10 , CYS A:13 , HIS A:32 , CYS A:35BINDING SITE FOR RESIDUE ZN A 998
2AC2SOFTWARECYS A:38 , CYS A:41 , CYS A:59 , HIS A:61BINDING SITE FOR RESIDUE ZN A 999

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G47)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1G47)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G47)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIM_DOMAIN_2PS50023 LIM domain profile.LIMS1_HUMAN8-69
71-128
191-250
133-190
251-310		  1A:8-69
-
-
-
-
2LIM_DOMAIN_1PS00478 LIM zinc-binding domain signature.LIMS1_HUMAN10-45
71-104
135-168
193-226		  1A:10-45
-
-
-

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3ENST000003933103ENSE00001514785chr2:109204922-109205084163LIMS1_HUMAN-00--
1.8aENST000003933108aENSE00002191959chr2:109276061-109276220160LIMS1_HUMAN1-52521A:1-5252
1.12aENST0000039331012aENSE00001618857chr2:109287237-10928730367LIMS1_HUMAN53-75231A:53-7018
1.14ENST0000039331014ENSE00001746358chr2:109288781-109288901121LIMS1_HUMAN75-115410--
1.15aENST0000039331015aENSE00002187125chr2:109289336-109289485150LIMS1_HUMAN115-165510--
1.16bENST0000039331016bENSE00001613279chr2:109292334-109292484151LIMS1_HUMAN165-215510--
1.17ENST0000039331017ENSE00001601331chr2:109293062-10929315493LIMS1_HUMAN216-246310--
1.18ENST0000039331018ENSE00001805893chr2:109294435-10929448349LIMS1_HUMAN247-263170--
1.19ENST0000039331019ENSE00001629219chr2:109297151-10929722676LIMS1_HUMAN263-288260--
1.21cENST0000039331021cENSE00001514784chr2:109300341-1093037023362LIMS1_HUMAN288-325380--

(-) 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:70
 aligned with LIMS1_HUMAN | P48059 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:70
                                    10        20        30        40        50        60        70
           LIMS1_HUMAN    1 MANALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPC 70
               SCOP domains d1g47a1 A:1-35                     d1g47a2 A:36-70                     SCOP domains
               CATH domains 1g47A00 A:1-70 Cysteine Rich Protein                                   CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................eee..eee.............hhhhh.eee..eeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------LIM_DOMAIN_2  PDB: A:8-69 UniProt: 8-69                       - PROSITE (1)
                PROSITE (2) ---------LIM_DOMAIN_1  PDB: A:10-45          ------------------------- PROSITE (2)
               Transcript 1 Exon 1.8a  PDB: A:1-52 UniProt: 1-52                Exon 1.12a         Transcript 1
                  1g47 A  1 MANALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPC 70
                                    10        20        30        40        50        60        70
   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
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G47)

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (LIMS1_HUMAN | P48059)
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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0007569    cell aging    An aging process that has as participant a cell after a cell has stopped dividing. Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469).
    GO:0034329    cell junction assembly    A cellular process that results in the aggregation, arrangement and bonding together of a set of components to form a cell junction.
    GO:0071560    cellular response to transforming growth factor beta stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a transforming growth factor beta stimulus.
    GO:0001837    epithelial to mesenchymal transition    A transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
    GO:0045184    establishment of protein localization    The directed movement of a protein to a specific location.
    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:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0010811    positive regulation of cell-substrate adhesion    Any process that increases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.
    GO:0051894    positive regulation of focal adhesion assembly    Any process that activates or increases the frequency, rate or extent of focal adhesion assembly, the establishment and maturation of focal adhesions.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:1900026    positive regulation of substrate adhesion-dependent cell spreading    Any process that activates or increases the frequency, rate or extent of substrate adhesion-dependent cell spreading.
    GO:0050678    regulation of epithelial cell proliferation    Any process that modulates the frequency, rate or extent of epithelial cell proliferation.
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:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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  1g47
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 Related Entries

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

UniProtKB/Swiss-Prot
        LIMS1_HUMAN | P48059: 1nyp 1u5s 2cor 2d8x 2kbx 3f6q 4hi8 4hi9

(-) Related Entries Specified in the PDB File

4884 CHEMICAL SHIFTS FOR THIS PROTEIN DOMAIN