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(-) Description

Title :  CRYSTAL STRUCTURE OF FGF20 DIMER
 
Authors :  J. Kalinina, M. Mohammadi
Date :  28 Oct 08  (Deposition) - 28 Jul 09  (Release) - 01 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Trefoil Fold, Growth Factor, Polymorphism, Secreted, Hormone (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Kalinina, S. A. Byron, H. P. Makarenkova, S. K. Olsen, A. V. Eliseenkova, W. J. Larochelle, M. Dhanabal, S. Blais, D. M. Ornitz, L. A. Day, T. A. Neubert, P. M. Pollock, M. Mohammadi
Homodimerization Controls The Fibroblast Growth Factor 9 Subfamily'S Receptor Binding And Heparan Sulfate-Dependent Diffusion In The Extracellular Matrix
Mol. Cell. Biol. V. 29 4663 2009
PubMed-ID: 19564416  |  Reference-DOI: 10.1128/MCB.01780-08
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FIBROBLAST GROWTH FACTOR 20
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBLR (DE3)
    Expression System Taxid562
    Expression System Vector TypePET24A
    GeneFGF20
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFGF-20

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:140 , LYS A:157 , ARG A:164BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREARG A:163 , ARG A:164 , ARG A:180 , ARG A:183BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREARG A:180 , LYS A:182BINDING SITE FOR RESIDUE SO4 A 303
4AC4SOFTWAREARG B:1163 , ARG B:1164 , ARG B:1180 , ARG B:1183BINDING SITE FOR RESIDUE SO4 B 300
5AC5SOFTWAREARG B:1176 , ARG B:1180 , LYS B:1182BINDING SITE FOR RESIDUE SO4 B 304
6AC6SOFTWAREARG B:1140 , LYS B:1157 , ARG B:1164BINDING SITE FOR RESIDUE SO4 B 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F1R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3F1R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric/Biological Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020946G116RFGF20_HUMANPolymorphism3793405A
B
G116
1116
R
2UniProtVAR_020947P175AFGF20_HUMANPolymorphism10089600A
B
P175
1175
A
3UniProtVAR_020948D206NFGF20_HUMANPolymorphism17550360A
B
D206
1206
N

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HBGF_FGFPS00247 HBGF/FGF family signature.FGF20_HUMAN125-148
 
  2A:125-148
B:1125-1148

(-) Exons   (0, 0)

(no "Exon" information available for 3F1R)

(-) 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:157
 aligned with FGF20_HUMAN | Q9NP95 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:157
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       
         FGF20_HUMAN     52 PGAAQLAHLHGILRRRQLYCRTGFHLQILPDGSVQGTRQDHSLFGILEFISVAVGLVSIRGVDSGLYLGMNDKGELYGSEKLTSECIFREQFEENWYNTYSSNIYKHGDTGRRYFVALNKDGTPRDGARSKRHQKFTHFLPRPVDPERVPELYKDLL  208
               SCOP domains d3f1ra_ A: automated matches                                                                                                                                  SCOP domains
               CATH domains 3f1rA00 A:52-208  [code=2.80.10.50, no name defined]                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhheeeeee...eeeee.....eeee........eeeeeeee..eeeeee.....eeee.....eeee...hhhh.eeeeeee..eeeeeeeeee......eee..........hhhhh...hhhh.eeee..hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------HBGF_FGF  PDB: A:125-148------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3f1r A   52 PGAAQLAHLHGILRRRQLYCRTGFHLQILPDGSVQGTRQDHSLFGILEFISVAVGLVSIRGVDSGLYLGMNDKGELYGSEKLTSECIFREQFEENWYNTYSSNIYKHGDTGRRYFVALNKDGTPRDGARSKRHQKFTHFLPRPVDPERVPELYKDLL  208
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       

Chain B from PDB  Type:PROTEIN  Length:157
 aligned with FGF20_HUMAN | Q9NP95 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:157
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       
         FGF20_HUMAN     52 PGAAQLAHLHGILRRRQLYCRTGFHLQILPDGSVQGTRQDHSLFGILEFISVAVGLVSIRGVDSGLYLGMNDKGELYGSEKLTSECIFREQFEENWYNTYSSNIYKHGDTGRRYFVALNKDGTPRDGARSKRHQKFTHFLPRPVDPERVPELYKDLL  208
               SCOP domains d3f1rb_ B: automated matches                                                                                                                                  SCOP domains
               CATH domains 3f1rB00 B:1052-1208  [code=2.80.10.50, no name defined]                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhheeeeee...eeeee.....eeee........eeeeeeee..eeeeee.....eeee.....eeee...hhhh.eeeeeee..eeeeeeeeee......eee..........hhhhh...hhhh.eeee..hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------R----------------------------------------------------------A------------------------------N-- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------HBGF_FGF                ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3f1r B 1052 PGAAQLAHLHGILRRRQLYCRTGFHLQILPDGSVQGTRQDHSLFGILEFISVAVGLVSIRGVDSGLYLGMNDKGELYGSEKLTSECIFREQFEENWYNTYSSNIYKHGDTGRRYFVALNKDGTPRDGARSKRHQKFTHFLPRPVDPERVPELYKDLL 1208
                                  1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201       

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F1R)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FGF20_HUMAN | Q9NP95)
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: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: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: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:0060113    inner ear receptor cell differentiation    The process in which relatively unspecialized cells, acquire specialized structural and/or functional features of inner ear receptor cells. Inner ear receptor cells are mechanorecptors found in the inner ear responsible for transducing signals involved in balance and sensory perception of sound.
    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:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0060043    regulation of cardiac muscle cell proliferation    Any process that modulates the frequency, rate or extent of cardiac muscle cell proliferation.
    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.
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

1g82 STRUCTURE OF FIBROBLAST GROWTH FACTOR 9
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