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(-) Description

Title :  CRYSTAL STRUCTURE OF FIBROBLAST GROWTH FACTOR 4 (FGF4)
 
Authors :  P. Bellosta, A. N. Plotnikov, A. V. Eliseenkova, C. Basilico, M. Mohammadi
Date :  29 Apr 01  (Deposition) - 15 Aug 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  B-Trefoil Fold, Hormone/Growth Factor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Bellosta, A. Iwahori, A. N. Plotnikov, A. V. Eliseenkova, C. Basilico, M. Mohammadi
Identification Of Receptor And Heparin Binding Sites In Fibroblast Growth Factor 4 By Structure-Based Mutagenesis.
Mol. Cell. Biol. V. 21 5946 2001
PubMed-ID: 11486033  |  Reference-DOI: 10.1128/MCB.21.17.5946-5957.2001
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FIBROBLAST GROWTH FACTOR 4
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentB-TREFOIL DOMAIN
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFGF4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:182 , LYS A:183 , LYS A:188 , HOH A:1029 , HOH A:1065 , HOH A:1066BINDING SITE FOR RESIDUE SO4 A 300
2AC2SOFTWAREARG A:103 , ARG A:123 , GLY A:124 , LYS A:144 , THR A:187 , HOH A:1000 , HOH A:1033 , HOH A:1035 , HOH A:1049BINDING SITE FOR RESIDUE SO4 A 301
3AC3SOFTWAREGLY A:79 , LYS A:81 , ASP A:110 , LYS A:173BINDING SITE FOR RESIDUE SO4 A 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HBGF_FGFPS00247 HBGF/FGF family signature.FGF4_HUMAN143-166  1A:143-166

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000001687121ENSE00001064298chr11:69590171-69589513659FGF4_HUMAN1-1141141A:79-11436
1.2ENST000001687122ENSE00001064299chr11:69588895-69588792104FGF4_HUMAN114-148351A:114-14835
1.3ENST000001687123ENSE00000991995chr11:69588253-69587797457FGF4_HUMAN149-206581A:149-20658

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:128
 aligned with FGF4_HUMAN | P08620 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:128
                                    88        98       108       118       128       138       148       158       168       178       188       198        
           FGF4_HUMAN    79 GIKRLRRLYCNVGIGFHLQALPDGRIGGAHADTRDSLLELSPVERGVVSIFGVASRFFVAMSSKGKLYGSPFFTDECTFKEILLPNNYNAYESYKYPGMFIALSKNGKTKKGNRVSPTMKVTHFLPRL 206
               SCOP domains d1ijta_ A: Fibroblast growth factor 4 (FGF4)                                                                                     SCOP domains
               CATH domains 1ijtA00 A:79-206  [code=2.80.10.50, no name defined]                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....eeeee.....eeee...hhhh.eeeeeee..eeeeee....eeeee.....eeee.......eeeeee.hhh.eeeee.................hhhhh...hhhh.eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------HBGF_FGF  PDB: A:143-166---------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:79-114 [INCOMPLETE]----------------------------------Exon 1.3  PDB: A:149-206 UniProt: 149-206                  Transcript 1 (1)
           Transcript 1 (2) -----------------------------------Exon 1.2  PDB: A:114-148           ---------------------------------------------------------- Transcript 1 (2)
                 1ijt A  79 GIKRLRRLYCNVGIGFHLQALPDGRIGGAHADTRDSLLELSPVERGVVSIFGVASRFFVAMSSKGKLYGSPFFTDECTFKEILLPNNYNAYESYKYPGMFIALGKNGKTKKGNRVSPTMKVTHFLPRL 206
                                    88        98       108       118       128       138       148       158       168       178       188       198        

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (40, 40)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FGF4_HUMAN | P08620)
molecular function
    GO:0016303    1-phosphatidylinositol-3-kinase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol + ATP = a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ADP + 2 H(+).
    GO:0005088    Ras guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005104    fibroblast growth factor receptor binding    Interacting selectively and non-covalently with the fibroblast growth factor receptor (FGFR).
    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:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0046934    phosphatidylinositol-4,5-bisphosphate 3-kinase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + ADP + 2 H(+).
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, 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:0060561    apoptotic process involved in morphogenesis    Any apoptotic process that contributes to the shaping of an anatomical structure.
    GO:0001502    cartilage condensation    The condensation of mesenchymal cells that have been committed to differentiate into chondrocytes.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0060591    chondroblast differentiation    The process in which a mesenchymal cell, acquires specialized structural and/or functional features of a chondroblast. Differentiation includes the processes involved in commitment of a cell to a chondroblast fate. A chondroblast is a precursor cell to chondrocytes.
    GO:0060363    cranial suture morphogenesis    The process in which any suture between cranial bones is generated and organized.
    GO:0035116    embryonic hindlimb morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the hindlimbs are generated and organized. The hindlimbs are the posterior limbs of an animal.
    GO:0030326    embryonic limb morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping.
    GO:0008543    fibroblast growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands.
    GO:0010463    mesenchymal cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0042475    odontogenesis of dentin-containing tooth    The process whose specific outcome is the progression of a dentin-containing tooth over time, from its formation to the mature structure. A dentin-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and is composed mainly of dentin, a dense calcified substance, covered by a layer of enamel.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0046854    phosphatidylinositol phosphorylation    The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol.
    GO:0036092    phosphatidylinositol-3-phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidylinositol-3-phosphate, a phosphatidylinositol monophosphate carrying the phosphate group at the 3-position.
    GO:0048015    phosphatidylinositol-mediated signaling    A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0051781    positive regulation of cell division    Any process that activates or increases the frequency, rate or extent of cell division.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    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:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:2000544    regulation of endothelial cell chemotaxis to fibroblast growth factor    Any process that modulates the frequency, rate or extent of endothelial cell chemotaxis to fibroblast growth factor.
    GO:0010468    regulation of gene expression    Any process that modulates 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:0014066    regulation of phosphatidylinositol 3-kinase signaling    Any process that modulates the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0019827    stem cell population maintenance    The process by which an organism or tissue maintains a population of stem cells of a single type. This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types.
cellular component
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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(-) Related Entries Specified in the PDB File

1ihk 1IHK IS THE CRYSTAL STRUCTURE OF FIBROBLAST GROWTH FACTOR 9 (FGF9)