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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN FHF1B (FGF12B)
 
Authors :  S. K. Olsen, M. Garbi, N. Zampieri, A. V. Eliseenkova, D. M. Ornitz, M. Goldfarb, M. Mohammadi
Date :  22 Jul 03  (Deposition) - 05 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Fgf-12; Human; Crystal Structure, Hormone/Growth Factor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. K. Olsen, M. Garbi, N. Zampieri, A. V. Eliseenkova, D. M. Ornitz, M. Goldfarb, M. Mohammadi
Fibroblast Growth Factor (Fgf) Homologous Factors Share Structural But Not Functional Homology With Fgfs
J. Biol. Chem. V. 278 34226 2003
PubMed-ID: 12815063  |  Reference-DOI: 10.1074/JBC.M303183200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FIBROBAST GROWTH FACTOR HOMOLOGOUS FACTOR 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-144
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsT7 PROMOTER DRIVEN EXPRESSION
    SynonymFGF-12

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:52 , LYS A:86 , GLU A:87 , SER A:88 , GLN A:104 , SER A:107 , ARG A:109BINDING SITE FOR RESIDUE SO4 A 437
2AC2SOFTWAREARG A:109 , ALA A:110 , PHE A:112 , ASN A:125 , ARG A:126 , LYS A:129 , HOH A:417BINDING SITE FOR RESIDUE SO4 A 438
3AC3SOFTWAREGLN A:19 , SER A:62 , LYS A:131 , PRO A:132 , SER A:133 , HOH A:409BINDING SITE FOR RESIDUE SO4 A 439
4AC4SOFTWARELEU A:51 , ARG A:52 , TYR A:72 , LYS A:123 , ARG A:126BINDING SITE FOR RESIDUE SO4 A 440

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q1U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q1U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076507R114HFGF12_HUMANDisease (EIEE47)  ---AR52H

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HBGF_FGFPS00247 HBGF/FGF family signature.FGF12_HUMAN133-156  1A:71-94

(-) Exons   (0, 0)

(no "Exon" information available for 1Q1U)

(-) 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:138
 aligned with FGF12_HUMAN | P61328 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:138
                                    77        87        97       107       117       127       137       147       157       167       177       187       197        
          FGF12_HUMAN    68 PQLKGIVTRLFSQQGYFLQMHPDGTIDGTKDENSDYTLFNLIPVGLRVVAIQGVKASLYVAMNGEGYLYSSDVFTPECKFKESVFENYYVIYSSTLYRQQESGRAWFLGLNKEGQIMKGNRVKKTKPSSHFVPKPIEV 205
               SCOP domains d1q1ua_ A: Fibrobast growth factor homologous factor 1 (FHF1b, FGF12b)                                                                     SCOP domains
               CATH domains 1q1uA00 A:6-143  [code=2.80.10.50, no name defined]                                                                                        CATH domains
               Pfam domains -----FGF-1q1uA01 A:11-137                                                                                                           ------ Pfam domains
         Sec.struct. author .....eeeeeee...eeeee.....eeee....hhhh.eeeeeee..eeeeee.....eeee.....eeee...hhhh.eeeeee...eeeeeeeeee......eee..........hhhhh...hhhh.eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------H------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------HBGF_FGF  PDB: A:71-94  ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1q1u A   6 PQLKGIVTRLFSQQGYFLQMHPDGTIDGTKDENSDYTLFNLIPVGLRVVAIQGVKASLYVAMNGEGYLYSSDVFTPECKFKESVFENYYVIYSSTLYRQQESGRAWFLGLNKEGQIMKGNRVKKTKPSSHFVPKPIEV 143
                                    15        25        35        45        55        65        75        85        95       105       115       125       135        

   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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Trefoil (131)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FGF12_HUMAN | P61328)
molecular function
    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:0044325    ion channel binding    Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
    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: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.
    GO:0017080    sodium channel regulator activity    Modulates the activity of a sodium channel.
biological process
    GO:0007254    JNK cascade    An intracellular protein kinase cascade containing at least a JNK (a MAPK), a JNKK (a MAPKK) and a JUN3K (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:0008344    adult locomotory behavior    Locomotory behavior in a fully developed and mature organism.
    GO:0086002    cardiac muscle cell action potential involved in contraction    An action potential that occurs in a cardiac muscle cell and is involved in its contraction.
    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:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    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:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:2001258    negative regulation of cation channel activity    Any process that stops, prevents or reduces the frequency, rate or extent of cation channel activity.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0050905    neuromuscular process    Any process pertaining to the functions of the nervous and muscular systems of an organism.
    GO:0010765    positive regulation of sodium ion transport    Any process that increases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0003254    regulation of membrane depolarization    Any process that modulates the rate, frequency or extent of membrane depolarization. Membrane depolarization is the process in which membrane potential changes in the depolarizing direction from the resting potential, usually from negative to positive.
    GO:1902305    regulation of sodium ion transmembrane transport    Any process that modulates the frequency, rate or extent of sodium ion transmembrane transport.
    GO:2000649    regulation of sodium ion transmembrane transporter activity    Any process that modulates the frequency, rate or extent of sodium ion transmembrane transporter activity.
    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: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: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.
    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.

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 Related Entries

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        FGF12_HUMAN | P613284jq0

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