Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  LEM DOMAIN OF HUMAN INNER NUCLEAR MEMBRANE PROTEIN EMERIN
 
Authors :  N. Wolff, B. Gilquin, K. Courchay, I. Callebaut, S. Zinn-Justin
Date :  18 Jun 01  (Deposition) - 04 Jul 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Emerin Nucleus Membrane Domain Dystrophy, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Wolff, B. Gilquin, K. Courchay, I. Callebaut, H. J. Worman, S. Zinn-Justin
Structural Analysis Of Emerin, An Inner Nuclear Membrane Protein Mutated In X-Linked Emery-Dreifuss Muscular Dystrophy
Febs Lett. V. 501 171 2001
PubMed-ID: 11470279  |  Reference-DOI: 10.1016/S0014-5793(01)02649-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EMERIN
    ChainsA
    EngineeredYES
    FragmentLEM DOMAIN (RESIDUES 2-54)
    Other DetailsCHEMICAL SYNTHESIS
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1JEI)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_005198S54FEMD_HUMANDisease (EDMD1)  ---AS53F

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003698421aENSE00001925261X:153607557-153607926370EMD_HUMAN1-28281A:1-2727
1.2bENST000003698422bENSE00001669344X:153608050-153608154105EMD_HUMAN28-63361A:27-5327
1.3aENST000003698423aENSE00001626504X:153608302-15360837978EMD_HUMAN63-89270--
1.3dENST000003698423dENSE00001687247X:153608594-153608727134EMD_HUMAN89-133450--
1.4bENST000003698424bENSE00001605338X:153609113-15360916250EMD_HUMAN134-150170--
1.4jENST000003698424jENSE00000868367X:153609242-153609883642EMD_HUMAN150-2541050--

(-) 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:53
 aligned with EMD_HUMAN | P50402 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:53
                                    11        21        31        41        51   
             EMD_HUMAN    2 DNYADLSDTELTTLLRRYNIPHGPVVGSTRRLYEKKIFEYETQRRRLSPPSSS 54
               SCOP domains d1jeia_ A: Inner nuclear membrane protein emerin      SCOP domains
               CATH domains 1jeiA00 A:1-53  [code=1.10.720.40, no name defined]   CATH domains
               Pfam domains LEM-1jeiA01 A:1-43                         ---------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh..........hhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------F SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:1-27     -------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.2b  PDB: A:27-53     Transcript 1 (2)
                  1jei A  1 DNYADLSDTELTTLLRRYNIPHGPVVGSTRRLYEKKIFEYETQRRRLSPPSSS 53
                                    10        20        30        40        50   

   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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: HeH (20)

(-) Gene Ontology  (22, 22)

NMR Structure(hide GO term definitions)
Chain A   (EMD_HUMAN | P50402)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0048487    beta-tubulin binding    Interacting selectively and non-covalently with the microtubule constituent protein beta-tubulin.
    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).
biological process
    GO:0071363    cellular response to growth factor 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 growth factor stimulus.
    GO:0007077    mitotic nuclear envelope disassembly    The cell cycle process in which the controlled breakdown of the nuclear envelope during mitotic cell division occurs.
    GO:0007084    mitotic nuclear envelope reassembly    The cell cycle process that results in reformation of the nuclear envelope during mitotic cell division.
    GO:0006936    muscle contraction    A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
    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:0035414    negative regulation of catenin import into nucleus    Any process that decreases the rate, frequency or extent of the directed movement of a catenin protein from the cytoplasm into the nucleus.
    GO:0048147    negative regulation of fibroblast proliferation    Any process that stops, prevents, or reduces the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
    GO:0046827    positive regulation of protein export from nucleus    Any process that activates or increases the frequency, rate or extent of directed movement of proteins from the nucleus into the cytoplasm.
    GO:0060828    regulation of canonical Wnt signaling pathway    Any process that modulates the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0035914    skeletal muscle cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle cell, a somatic cell located in skeletal muscle.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    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:0005637    nuclear inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0005640    nuclear outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes.
    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.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1jei)
 
  Sites
(no "Sites" information available for 1jei)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1jei)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1jei
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  EMD_HUMAN | P50402
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  310300
    Disease InformationOMIM
 
Access by GenAge ID
  0121
    Age Related InformationGenAge
  0123
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  EMD_HUMAN | P50402
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        EMD_HUMAN | P504022odc 2odg

(-) Related Entries Specified in the PDB File

1h9e 1H9E CONTAINS LEM-LIKE DOMAIN OF HUMAN INNER NUCLEAR MEMBRANE PROTEIN LAP2
1h9f 1H9F CONTAINS LEM DOMAIN OF HUMAN INNER NUCLEAR MEMBRANE PROTEIN LAP2