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(-) Description

Title :  SOLUTION STRUCTURE OF THE C-TERMINAL PH DOMAIN OF FYVE, RHOGEF AND PH DOMAIN CONTAINING PROTEIN 3 (FGD3) FROM HUMAN
 
Authors :  H. Li, T. Tomizawa, N. Tochio, Y. Muto, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  17 May 05  (Deposition) - 17 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Fyve, Rhogef And Ph Domain Containing Protein 3, Ph Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Li, T. Tomizawa, N. Tochio, Y. Muto, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The C-Terminal Ph Domain Of Fyve, Rhogef And Ph Domain Containing Protein 3 (Fgd3) From Human
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FYVE, RHOGEF AND PH DOMAIN CONTAINING PROTEIN 3
    ChainsA
    EngineeredYES
    Expression System PlasmidP050125-03
    Expression System Vector TypePLASMID
    FragmentPH DOMAIN
    GeneFGD3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymZINC FINGER FYVE DOMAIN CONTAINING PROTEIN 5

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2COC)

(-) Sites  (0, 0)

(no "Site" information available for 2COC)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2COC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2COC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2COC)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.FGD3_HUMAN370-469
604-703
  1-
A:8-106

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003754821ENSE00001467240chr9:95709733-95710011279FGD3_HUMAN-00--
1.4aENST000003754824aENSE00001410773chr9:95737520-95737687168FGD3_HUMAN-00--
1.5ENST000003754825ENSE00002195894chr9:95738490-95738991502FGD3_HUMAN1-1511510--
1.6ENST000003754826ENSE00001091502chr9:95765207-9576529690FGD3_HUMAN152-181300--
1.7ENST000003754827ENSE00001091495chr9:95766283-95766419137FGD3_HUMAN182-227460--
1.8ENST000003754828ENSE00001091498chr9:95768306-95768462157FGD3_HUMAN227-279530--
1.9ENST000003754829ENSE00000869896chr9:95772528-95772666139FGD3_HUMAN280-326470--
1.10ENST0000037548210ENSE00000869895chr9:95773496-9577355459FGD3_HUMAN326-345200--
1.11ENST0000037548211ENSE00000900686chr9:95776134-95776280147FGD3_HUMAN346-394490--
1.12bENST0000037548212bENSE00000869893chr9:95778019-9577811193FGD3_HUMAN395-425310--
1.13bENST0000037548213bENSE00000869892chr9:95780418-9578049780FGD3_HUMAN426-452270--
1.14ENST0000037548214ENSE00000869891chr9:95782113-9578214331FGD3_HUMAN452-462110--
1.15ENST0000037548215ENSE00000869890chr9:95782599-95782706108FGD3_HUMAN463-498360--
1.16ENST0000037548216ENSE00000869889chr9:95784609-9578467163FGD3_HUMAN499-519211A:1-77
1.17ENST0000037548217ENSE00000900692chr9:95792156-95792278123FGD3_HUMAN520-560410--
1.19aENST0000037548219aENSE00001091500chr9:95795051-95795155105FGD3_HUMAN561-595350--
1.19dENST0000037548219dENSE00001337184chr9:95796823-95796963141FGD3_HUMAN596-642471A:8-4538
1.20ENST0000037548220ENSE00001467220chr9:95797620-95798518899FGD3_HUMAN643-725831A:46-112 (gaps)70

(-) 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:112
 aligned with FGD3_HUMAN | Q5JSP0 from UniProtKB/Swiss-Prot  Length:725

    Alignment length:200
                                   522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712
           FGD3_HUMAN   513 GSSGAAGLEPRKLSSKTRRDKEKQSCKSCGETFNSITKRRHHCKLCGAVICGKCSEFKAENSRQSRVCRDCFLTQPVAPESTEKTPTADPQPSLLCGPLRLSESGETWSEVWAAIPMSDPQVLHLQGGSQDGRLPRTIPLPSCKLSVPDPEERLDSGHVWKLQWAKQSWYLSASSAELQQQWLETLSTAAHGDTAQDSPG 712
               SCOP domains --------------------------------------------------------------------------------------------d2coca1 A:8-106 FYVE, RhoGEF and PH domain containing protein 3, FGD3                              --------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......-------------------------------------------------------------------------------------...eeeeeee.....eeeeeeeee.....eeeee.........eee.....eee...........eeeeeee..eeeeeee..hhhhhhhhhhhhhhh.---...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------PH_DOMAIN  PDB: A:8-106 UniProt: 604-703                                                            --------- PROSITE
               Transcript 1 1.16   Exon 1.17  PDB: - UniProt: 520-560       Exon 1.19a  PDB: - UniProt: 561-595Exon 1.19d  PDB: A:8-45 UniProt: 596-642       Exon 1.20  PDB: A:46-112 (gaps) UniProt: 643-725 [INCOMPLETE]          Transcript 1
                 2coc A   1 GSSGSSG-------------------------------------------------------------------------------------SLLCGPLRLSESGETWSEVWAAIPMSDPQVLHLQGGSQDGRLPRTIPLPSCKLSVPDPEERLDSGHVWKLQWAKQSWYLSASSAELQQQWLETLSTAAH---SGPSSG 112
                                  |  -         -         -         -         -         -         -         -         -  |     15        25        35        45        55        65        75        85        95       105|   |  112
                                  7                                                                                     8                                                                                               106 107     

   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  (0, 0)

(no "CATH Domain" information available for 2COC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2COC)

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (FGD3_HUMAN | Q5JSP0)
molecular function
    GO:0005089    Rho guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. 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:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. 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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0031267    small GTPase binding    Interacting selectively and non-covalently with a small monomeric GTPase.
biological process
    GO:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0007010    cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:0046847    filopodium assembly    The assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0043087    regulation of GTPase activity    Any process that modulates the rate of GTP hydrolysis by a GTPase.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0051056    regulation of small GTPase mediated signal transduction    Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

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