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(-) Description

Title :  SOLUTION STRUCTURE OF IMMUNOGLOBULIN LIKE DOMAIN OF MOUSE NUCLEAR LAMIN
 
Authors :  N. Kobayashi, T. Kigawa, S. Koshiba, M. Inoue, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  29 May 03  (Deposition) - 22 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Immunoglobulin Like Fold, Nuclear Lamin, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Kobayashi, T. Kigawa, S. Koshiba, M. Inoue, S. Yokoyama
Solution Structure Of Immunoglobulin Like Domain Of Mouse Nuclear Lamin
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LAMIN A
    ChainsA
    EngineeredYES
    Expression System PlasmidP011206-07
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL IMMUNOGLOBULIN LIKE DOMAIN
    GeneRIKEN CDNA 1200006N04
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymNUCLEAR LAMIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1UFG)

(-) Sites  (0, 0)

(no "Site" information available for 1UFG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Pro A:108 -Pro A:109

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UFG)

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3cENSMUST000000296993cENSMUSE00000721382chr3:88307257-88306670588LMNA_MOUSE1-1191190--
1.5ENSMUST000000296995ENSMUSE00000419377chr3:88292353-88292197157LMNA_MOUSE119-171530--
1.6ENSMUST000000296996ENSMUSE00000175618chr3:88290855-88290730126LMNA_MOUSE172-213420--
1.7ENSMUST000000296997ENSMUSE00000175619chr3:88290552-88290382171LMNA_MOUSE214-270570--
1.8ENSMUST000000296998ENSMUSE00000175620chr3:88290251-88290126126LMNA_MOUSE271-312420--
1.9ENSMUST000000296999ENSMUSE00000175616chr3:88289069-88288849221LMNA_MOUSE313-386740--
1.10ENSMUST0000002969910ENSMUSE00000175611chr3:88288759-88288537223LMNA_MOUSE386-460751A:1-60 (gaps)61
1.11bENSMUST0000002969911bENSMUSE00000175613chr3:88288076-88287969108LMNA_MOUSE461-496361A:61-9636
1.12ENSMUST0000002969912ENSMUSE00000175612chr3:88287868-88287749120LMNA_MOUSE497-536401A:97-13640
1.13aENSMUST0000002969913aENSMUSE00000175621chr3:88287335-8828724096LMNA_MOUSE537-568321A:137-1459
1.14bENSMUST0000002969914bENSMUSE00000500596chr3:88286534-88286268267LMNA_MOUSE569-657891A:146-151 (gaps)41
1.15cENSMUST0000002969915cENSMUSE00000820828chr3:88286022-88285070953LMNA_MOUSE658-66580--

(-) 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:151
 aligned with LMNA_MOUSE | P48678 from UniProtKB/Swiss-Prot  Length:665

    Alignment length:216
                                   409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609      
           LMNA_MOUSE   400 GRASSHSSQSQGGGSVTKKRKLESSESRSSFSQHARTSGRVAVEEVDEEGKFVRLRNKSNEDQSMGNWQIRRQNGDDPLMTYRFPPKFTLKAGQVVTIWASGAGATHSPPTDLVWKAQNTWGCGSSLRTALINSTGEEVAMRKLVRSLTMVEDNEDDDEDGEELLHHHRGSHCSGSGDPAEYNLRSRTVLCGTCGQPADKAAGGAGAQVGGSISSG 615
               SCOP domains d 1ufga_ A: Lamin A/C globular tail domain                                                                                                                                                                               SCOP domains
               CATH domains 1 ufgA00 A:1-151  [code=2.60.40.1260, no name defined]                                                                                                                                                                   CATH domains
               Pfam domains -----------------------------LTD-1ufgA01 A:29-145                                                                                                 ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .-...............................eeee...eeeeee.....eeeeee.....ee....eeeeee.....eeee.....ee....eeeeee...........eeee..........eeeeeee.....eeeeeeee.-----------------------------..-.----------------------------------... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.10  PDB: A:1-60 (gaps) UniProt: 386-460 [INCOMPLETE]  Exon 1.11b  PDB: A:61-96            Exon 1.12  PDB: A:97-136                Exon 1.13a  PDB: A:137-145      Exon 1.14b  PDB: A:146-151 (gaps) [INCOMPLETE]  Transcript 1
                 1ufg A   1 G-SSGSSGQSQGGGSVTKKRKLESSESRSSFSQHARTSGRVAVEEVDEEGKFVRLRNKSNEDQSMGNWQIRRQNGDDPLMTYRFPPKFTLKAGQVVTIWASGAGATHSPPTDLVWKAQNTWGCGSSLRTALINSTGEEVAMRKLVR-----------------------------SG-P----------------------------------SSG 151
                            | |      9        19        29        39        49        59        69        79        89        99       109       119       129       139     |   -         -         -     || |-         -         -         -   |  
                            | 2                                                                                                                                            145                           146| |                                149  
                            1                                                                                                                                                                             147 |                                     
                                                                                                                                                                                                            148                                     

   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, 1)

NMR Structure

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (33, 33)

NMR Structure(hide GO term definitions)
Chain A   (LMNA_MOUSE | P48678)
molecular function
    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:0008157    protein phosphatase 1 binding    Interacting selectively and non-covalently with the enzyme protein phosphatase 1.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0071456    cellular response to hypoxia    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 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:0030010    establishment of cell polarity    The specification and formation of anisotropic intracellular organization or cell growth patterns.
    GO:0030951    establishment or maintenance of microtubule cytoskeleton polarity    Any cellular process that results in the specification, formation or maintenance of polarized microtubule-based cytoskeletal structures.
    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:1904178    negative regulation of adipose tissue development    Any process that stops, prevents or reduces the frequency, rate or extent of adipose tissue development.
    GO:2001237    negative regulation of extrinsic apoptotic signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway.
    GO:0072201    negative regulation of mesenchymal cell proliferation    Any process that decreases the frequency, rate or extent of mesenchymal cell proliferation. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets.
    GO:0090201    negative regulation of release of cytochrome c from mitochondria    Any process that decreases the rate, frequency or extent of release of cytochrome c from mitochondria, the process in which cytochrome c is enabled to move from the mitochondrial intermembrane space into the cytosol, which is an early step in apoptosis and leads to caspase activation.
    GO:0006998    nuclear envelope organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope.
    GO:0006997    nucleus organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.
    GO:0090343    positive regulation of cell aging    Any process that increases the rate, frequency, or extent of cell aging. Cell aging is the progression of the cell from its inception to the end of its lifespan.
    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:0045669    positive regulation of osteoblast differentiation    Any process that activates or increases the frequency, rate or extent of osteoblast differentiation.
    GO:0034504    protein localization to nucleus    A process in which a protein transports or maintains the localization of another protein to the nucleus.
    GO:0030334    regulation of cell migration    Any process that modulates the frequency, rate or extent of cell migration.
    GO:1900180    regulation of protein localization to nucleus    Any process that modulates the frequency, rate or extent of protein localization to nucleus.
    GO:0009612    response to mechanical stimulus    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 mechanical stimulus.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0035105    sterol regulatory element binding protein import into nucleus    The transfer of a sterol regulatory element binding protein (SREBP) into the nucleus, across the nuclear membrane, in response to altered levels of one or more lipids. SREBPs are transcription factors that bind sterol regulatory elements (SREs), DNA motifs found in the promoters of target genes.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005882    intermediate filament    A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins.
    GO:0005638    lamin filament    Any of a group of intermediate-filament proteins that form the fibrous matrix on the inner surface of the nuclear envelope. They are classified as lamins A, B and C.
    GO:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0005652    nuclear lamina    The fibrous, electron-dense layer lying on the nucleoplasmic side of the inner membrane of a cell nucleus, composed of lamin filaments. The polypeptides of the lamina are thought to be concerned in the dissolution of the nuclear envelope and its re-formation during mitosis. The lamina is composed of lamin A and lamin C filaments cross-linked into an orthogonal lattice, which is attached via lamin B to the inner nuclear membrane through interactions with a lamin B receptor, an IFAP, in the membrane.
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    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.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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