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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN FIBROBLAST GROWTH FACTOR HOMOLOGOUS FACTOR 2A (FHF2A), ALSO REFERRED TO AS FIBROBLAST GROWTH FACTOR 13A (FGF13A)
 
Authors :  M. Mohammadi
Date :  05 May 09  (Deposition) - 26 May 09  (Release) - 28 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta-Trefoil Fold, Alternative Splicing, Growth Factor, Polymorphism, Hormone (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Goetz, K. Dover, F. Laezza, N. Shtraizent, X. Huang, D. Tchetchik, A. V. Eliseenkova, C. F. Xu, T. A. Neubert, D. M. Ornitz, M. Goldfarb, M. Mohammadi
Crystal Structure Of A Fibroblast Growth Factor Homologous Factor (Fhf) Defines A Conserved Surface On Fhfs For Binding And Modulation Of Voltage-Gated Sodium Channels.
J. Biol. Chem. V. 284 17883 2009
PubMed-ID: 19406745  |  Reference-DOI: 10.1074/JBC.M109.001842
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FIBROBLAST GROWTH FACTOR 13
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30(A)
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 53-245
    GeneFGF13, FHF2, FIBROBLAST GROWTH FACTOR HOMOLOGOUS FACTOR 2 (FHF2)
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFGF-13, FIBROBLAST GROWTH FACTOR HOMOLOGOUS FACTOR 2, FHF-2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3HBW)

(-) Sites  (0, 0)

(no "Site" information available for 3HBW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020945K197QFGF13_HUMANPolymorphism17510270A
B
K197
1197
Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020945K197QFGF13_HUMANPolymorphism17510270A
A
K197
1197
Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020945K197QFGF13_HUMANPolymorphism17510270A
B
K197
1197
Q

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HBGF_FGFPS00247 HBGF/FGF family signature.FGF13_HUMAN129-152
 
  2A:129-152
B:1129-1152
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HBGF_FGFPS00247 HBGF/FGF family signature.FGF13_HUMAN129-152
 
  1A:129-152
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HBGF_FGFPS00247 HBGF/FGF family signature.FGF13_HUMAN129-152
 
  1-
B:1129-1152

(-) Exons   (0, 0)

(no "Exon" information available for 3HBW)

(-) Sequences/Alignments

Asymmetric 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:149
 aligned with FGF13_HUMAN | Q92913 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:149
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203         
         FGF13_HUMAN     64 PQLKGIVTKLYSRQGYHLQLQADGTIDGTKDEDSTYTLFNLIPVGLRVVAIQGVQTKLYLAMNSEGYLYTSELFTPECKFKESVFENYYVTYSSMIYRQQQSGRGWYLGLNKEGEIMKGNHVKKNKPAAHFLPKPLKVAMYKEPSLHDL  212
               SCOP domains d3hbwa_ A: automated matches                                                                                                                          SCOP domains
               CATH domains 3hbwA00 A:64-212  [code=2.80.10.50, no name defined]                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....eeee.....eeee....hhhh.eeeeeee..eeeeee.....eeee.....eeee...hhh.eeeeeee...eeeeeeeeee......eee..........hhhhh...hhhh.eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------HBGF_FGF  PDB: A:129-152------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3hbw A   64 PQLKGIVTKLYSRQGYHLQLQADGTIDGTKDEDSTYTLFNLIPVGLRVVAIQGVQTKLYLAMNSEGYLYTSELFTPECKFKESVFENYYVTYSSMIYRQQQSGRGWYLGLNKEGEIMKGNHVKKNKPAAHFLPKPLKVAMYKEPSLHDL  212
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203         

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with FGF13_HUMAN | Q92913 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:149
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203         
         FGF13_HUMAN     64 PQLKGIVTKLYSRQGYHLQLQADGTIDGTKDEDSTYTLFNLIPVGLRVVAIQGVQTKLYLAMNSEGYLYTSELFTPECKFKESVFENYYVTYSSMIYRQQQSGRGWYLGLNKEGEIMKGNHVKKNKPAAHFLPKPLKVAMYKEPSLHDL  212
               SCOP domains d3hbwb_ B: automated matches                                                                                                                          SCOP domains
               CATH domains 3hbwB00 B:1064-1212  [code=2.80.10.50, no name defined]                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....eeee.....eeee....hhhh.eeeeeee..eeeeee.....eeee.....eeee...hhh.eeeeeee...eeeeeeeeee......eee..........hhhhh...hhhh.eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------Q--------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------HBGF_FGF                ------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3hbw B 1064 PQLKGIVTKLYSRQGYHLQLQADGTIDGTKDEDSTYTLFNLIPVGLRVVAIQGVQTKLYLAMNSEGYLYTSELFTPECKFKESVFENYYVTYSSMIYRQQQSGRGWYLGLNKEGEIMKGNHVKKNKPAAHFLPKPLKVAMYKEPSLHDL 1212
                                  1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203         

   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 Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (37, 37)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FGF13_HUMAN | Q92913)
molecular function
    GO:0048487    beta-tubulin binding    Interacting selectively and non-covalently with the microtubule constituent protein beta-tubulin.
    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: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:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    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:0030295    protein kinase activator activity    Binds to and increases the activity of a protein kinase, an enzyme which phosphorylates a protein.
    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: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:0032147    activation of protein kinase activity    Any process that initiates the activity of an inactive protein kinase.
    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:0021795    cerebral cortex cell migration    The orderly movement of cells from one site to another in the cerebral cortex.
    GO:0045200    establishment of neuroblast polarity    The specification and formation of the apicobasal polarity of a neuroblast cell, a progenitor of the central nervous system.
    GO:0021766    hippocampus development    The progression of the hippocampus over time from its initial formation until its mature state.
    GO:0007612    learning    Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.
    GO:0007613    memory    The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).
    GO:0046785    microtubule polymerization    The addition of tubulin heterodimers to one or both ends of a microtubule.
    GO:0048671    negative regulation of collateral sprouting    Any process that stops, prevents, or reduces the frequency, rate or extent of collateral sprouting.
    GO:0007026    negative regulation of microtubule depolymerization    Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule depolymerization; prevention of depolymerization of a microtubule can result from binding by 'capping' at the plus end (e.g. by interaction with another cellular protein of structure) or by exposing microtubules to a stabilizing drug such as taxol.
    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:0001764    neuron migration    The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature.
    GO:0072659    protein localization to plasma membrane    A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane.
    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:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    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:0030175    filopodium    Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    GO:0014704    intercalated disc    A complex cell-cell junction at which myofibrils terminate in cardiomyocytes; mediates mechanical and electrochemical integration between individual cardiomyocytes. The intercalated disc contains regions of tight mechanical attachment (fasciae adherentes and desmosomes) and electrical coupling (gap junctions) between adjacent cells.
    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:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.
    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.

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 Related Entries

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

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        FGF13_HUMAN | Q929134dck 4jpz

(-) Related Entries Specified in the PDB File

1q1u CRYSTAL STRUCTURE OF FIBROBLAST GROWTH FACTOR HOMOLOGOUS FACTOR 1B (FHF1B), ALSO REFERRED TO AS FIBROBLAST GROWTH FACTOR 12B (FGF12B)