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 :  SOLUTION STRUCTURE THE MEGF/TGFALPHA44-50 CHIMERIC GROWTH FACTOR
 
Authors :  S. G. Chamberlin, L. Brennan, S. M. Puddicombe, D. E. Davies, D. L. Turner
Date :  08 Aug 01  (Deposition) - 08 Aug 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Growth Factor, Egf Growth Factor, Chimeric (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Chamberlin, L. Brennan, S. Puddicombe, D. Davies, D. Turner
Solution Structure Of The Megf/Tgfalpha44-50 Chimeric Growth Factor.
Eur. J. Biochem. V. 268 6247 2001
PubMed-ID: 11733021  |  Reference-DOI: 10.1046/J.0014-2956.2001.02581.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MEGF/TGFALPHA44-50 CHIMERA
    ChainsA
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsTHE PROTEIN IS A CHIMERA OF EPIDERMAL GROWTH FACTOR RESIDUES 977-1018 AND HUMAN TRANSFORMING GROWTH FACTOR ALPHA RESIDUES 83-89
    SynonymEPIDERMAL GROWTH FACTOR AND TRANSFORMING GROWTH FACTOR ALPHA

 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 1GK5)

(-) Sites  (0, 0)

(no "Site" information available for 1GK5)

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:6 -A:20
2A:14 -A:31
3A:33 -A:42

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GK5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GK5)

(-) PROSITE Motifs  (3, 3)

NMR Structure (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EGF_3PS50026 EGF-like domain profile.TGFA_HUMAN43-83  1A:6-43
EGF_MOUSE362-402
838-876
877-918
919-959
978-1019
  1-
-
-
-
A:2-42
2EGF_1PS00022 EGF-like domain signature 1.TGFA_HUMAN71-82  1A:31-42
EGF_MOUSE1007-1018  1A:31-42
3EGF_2PS01186 EGF-like domain signature 2.TGFA_HUMAN71-82  1A:31-42
EGF_MOUSE386-401
467-482
771-786
862-875
904-917
1007-1018
  1-
-
-
-
-
A:31-42

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002954002aENSE00001855336chr2:70781147-70780860288TGFA_HUMAN1-14140--
1.4ENST000002954004ENSE00001164088chr2:70742044-7074199154TGFA_HUMAN14-32191A:1-22
1.5aENST000002954005aENSE00001129794chr2:70692868-70692748121TGFA_HUMAN32-72411A:3-3230
1.7bENST000002954007bENSE00002188045chr2:70683620-70683471150TGFA_HUMAN72-122511A:32-4918
1.8ENST000002954008ENSE00001129787chr2:70680459-70680350110TGFA_HUMAN122-159380--
1.10dENST0000029540010dENSE00001849780chr2:70677998-706744123587TGFA_HUMAN159-16020--

(-) 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:49
 aligned with EGF_MOUSE | P01132 from UniProtKB/Swiss-Prot  Length:1217

    Alignment length:65
                                   986       996      1006      1016      1026      1036     
           EGF_MOUSE    977 NSYPGCPSSYDGYCLNGGVCMHIESLDSYTCNCVIGYSGDRCQTRDLRWWELRHAGYGQKHDIMV 1041
               SCOP domains d1gk5a_ A: Epidermal growth factor, EGF                           SCOP domains
               CATH domains 1gk5A00 A:1-49 Laminin                                            CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeee....eeeee......hhhhh----------..------.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -EGF_3  PDB: A:2-42 UniProt: 978-1019      ---------------------- PROSITE (1)
                PROSITE (2) ------------------------------EGF_2       ----------------------- PROSITE (2)
                PROSITE (3) ------------------------------EGF_1       ----------------------- PROSITE (3)
                 Transcript ----------------------------------------------------------------- Transcript
                1gk5 A    1 NSYPGCPSSYDGYCLNGGVCMHIESLDSYTCNCVIGYSGDRCE----------HA------DLLA   49
                                    10        20        30        40  |      -   ||    - |   
                                                                     43         44|     46   
                                                                                 45          

Chain A from PDB  Type:PROTEIN  Length:49
 aligned with TGFA_HUMAN | P01135 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:66
                                                              59                              
                                                            58 |                              
                                    34        44        54   | |  63        73        83      
          TGFA_HUMAN     25 NSTSPLSADPPVAAAVVSHFNDCPDSHTQFCFHG-TCRFLVQEDKPACVCHSGYVGARCEHADLLA   89
               SCOP domains d1                 gk5a_ A: Epidermal growth factor, EGF           SCOP domains
               CATH domains 1g                 k5A00 A:1-49 Laminin                            CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..-----------------................eeeee....eeeee......hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------------------EGF_3  PDB: A:6-43 UniProt: 43-83         ------ PROSITE (1)
                PROSITE (2) -----------------------------------------------EGF_2       ------- PROSITE (2)
                PROSITE (3) -----------------------------------------------EGF_1       ------- PROSITE (3)
           Transcript 1 (1) Exon 1.4----------------------------------------Exon 1.7b          Transcript 1 (1)
           Transcript 1 (2) -------Exon 1.5a  PDB: A:3-32 UniProt: 32-72     ----------------- Transcript 1 (2)
                1gk5 A    1 NS-----------------YPGCPSSYDGYCLNGGVCMHIESLDSYTCNCVIGYSGDRCEHADLLA   49
                             |       -         3        13        23        33        43      
                             2                 3                                              

   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  (0, 0)

(no "Pfam Domain" information available for 1GK5)

(-) Gene Ontology  (60, 71)

NMR Structure(hide GO term definitions)
Chain A   (EGF_MOUSE | P01132)
molecular function
    GO:0042813    Wnt-activated receptor activity    Combining with a Wnt protein and transmitting the signal across the plasma membrane to initiate a change in cell activity.
    GO:0017147    Wnt-protein binding    Interacting selectively and non-covalently with Wnt-protein, a secreted growth factor involved in signaling.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0005154    epidermal growth factor receptor binding    Interacting selectively and non-covalently with the epidermal growth factor receptor.
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    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:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
biological process
    GO:0070371    ERK1 and ERK2 cascade    An intracellular protein kinase cascade containing at least ERK1 or ERK2 (MAPKs), a MEK (a MAPKK) and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0007262    STAT protein import into nucleus    The directed movement of dimerized STAT (Signal Transducers and Activators of Transcription) proteins into the nucleus following activation by members of the janus activated kinase (JAK) family of tyrosine kinases.
    GO:0044332    Wnt signaling pathway involved in dorsal/ventral axis specification    The series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of the target cell contributing to the establishment, maintenance and elaboration of the dorsal/ventral axis.
    GO:0000187    activation of MAPK activity    The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
    GO:0000186    activation of MAPKK activity    The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK).
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0048754    branching morphogenesis of an epithelial tube    The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder.
    GO:0060070    canonical Wnt signaling pathway    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. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
    GO:0007173    epidermal growth factor receptor signaling pathway    A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0060749    mammary gland alveolus development    The progression of the mammary gland alveolus over time, from its formation to its mature state. The mammary gland alveolus is a sac-like structure that is found in the mature gland.
    GO:0090370    negative regulation of cholesterol efflux    Any process that decreases the frequency, rate or extent of cholesterol efflux. Cholesterol efflux is the directed movement of cholesterol, cholest-5-en-3-beta-ol, out of a cell or organelle.
    GO:0051048    negative regulation of secretion    Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a substance from a cell or a tissue.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0043388    positive regulation of DNA binding    Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    GO:0035413    positive regulation of catenin import into nucleus    Any process that increases the rate, frequency or extent of the directed movement of a catenin protein from the cytoplasm into the nucleus.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0021940    positive regulation of cerebellar granule cell precursor proliferation    The process that activates or increases the rate or extent of granule cell precursor proliferation.
    GO:0045741    positive regulation of epidermal growth factor-activated receptor activity    Any process that activates or increases the frequency, rate or extent of EGF-activated receptor activity.
    GO:1900127    positive regulation of hyaluronan biosynthetic process    Any process that activates or increases the frequency, rate or extent of hyaluronan biosynthetic process.
    GO:0045840    positive regulation of mitotic nuclear division    Any process that activates or increases the frequency, rate or extent of mitosis.
    GO:0010800    positive regulation of peptidyl-threonine phosphorylation    Any process that increases the frequency, rate or extent of peptidyl-threonine phosphorylation. Peptidyl-threonine phosphorylation is the phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
    GO:0050731    positive regulation of peptidyl-tyrosine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0042327    positive regulation of phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
    GO:0061098    positive regulation of protein tyrosine kinase activity    Any process that increases the rate, frequency, or extent of protein tyrosine kinase activity.
    GO:2000060    positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process    Any process that activates or increases the frequency, rate or extent of protein ubiquitination involved in ubiquitin-dependent protein catabolic process.
    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:0090279    regulation of calcium ion import    Any process that modulates the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle.
    GO:0050730    regulation of peptidyl-tyrosine phosphorylation    Any process that modulates the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:2000008    regulation of protein localization to cell surface    Any process that modulates the frequency, rate or extent of protein localization to the cell surface.
    GO:0051223    regulation of protein transport    Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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:0005765    lysosomal membrane    The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    GO:0043235    receptor complex    Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

Chain A   (TGFA_HUMAN | P01135)
molecular function
    GO:0005154    epidermal growth factor receptor binding    Interacting selectively and non-covalently with the epidermal growth factor receptor.
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    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:0048208    COPII vesicle coating    The addition of COPII proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat.
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0000187    activation of MAPK activity    The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0051781    positive regulation of cell division    Any process that activates or increases the frequency, rate or extent of cell division.
    GO:0045741    positive regulation of epidermal growth factor-activated receptor activity    Any process that activates or increases the frequency, rate or extent of EGF-activated receptor activity.
    GO:0050679    positive regulation of epithelial cell proliferation    Any process that activates or increases the rate or extent of epithelial cell proliferation.
    GO:0045840    positive regulation of mitotic nuclear division    Any process that activates or increases the frequency, rate or extent of mitosis.
cellular component
    GO:0012507    ER to Golgi transport vesicle membrane    The lipid bilayer surrounding a vesicle transporting substances from the endoplasmic reticulum to the Golgi.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0033116    endoplasmic reticulum-Golgi intermediate compartment membrane    The lipid bilayer surrounding any of the compartments of the endoplasmic reticulum (ER)-Golgi intermediate compartment system.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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:0005887    integral component of plasma membrane    The component of the plasma 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: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.

 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 1gk5)
 
  Sites
(no "Sites" information available for 1gk5)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1gk5)
 

(-) 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
  1gk5
    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
  EGF_MOUSE | P01132
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  TGFA_HUMAN | P01135
    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)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    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
  EGF_MOUSE | P01132
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TGFA_HUMAN | P01135
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        EGF_MOUSE | P011321a3p 1egf 1epg 1eph 1epi 1epj 3egf
        TGFA_HUMAN | P011351mox 1p9j 1yuf 1yug 2tgf 3e50 3tgf 4tgf 5kn5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1GK5)