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(-) Description

Title :  SOLUTION STRUCTURE OF SH3 DOMAIN IN RHO-GTPASE-ACTIVATING PROTEIN 4
 
Authors :  W. Tanabe, K. Tsuda, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  29 Mar 07  (Deposition) - 02 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Sh3 Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Tanabe, K. Tsuda, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of Sh3 Domain In Rho-Gtpase-Activating Protein 4
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RHO GTPASE-ACTIVATING PROTEIN 4
    ChainsA
    EngineeredYES
    Expression System PlasmidP060130-05
    Expression System Vector TypePLASMID
    FragmentSH3 DOMAIN
    GeneARHGAP4, KIAA0131, RGC1, RHOGAP4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymRHO-GAP HEMATOPOIETIC PROTEIN C1, P115

 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 2EPD)

(-) Sites  (0, 0)

(no "Site" information available for 2EPD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.RHG04_HUMAN746-805  1A:747-805

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.10dENST0000035006010dENSE00002179871X:153191698-153191590109RHG04_HUMAN1-23230--
1.12ENST0000035006012ENSE00001799706X:153187262-153187058205RHG04_HUMAN23-91690--
1.13aENST0000035006013aENSE00001592943X:153186980-153186818163RHG04_HUMAN91-145550--
1.14bENST0000035006014bENSE00001690378X:153186612-15318655063RHG04_HUMAN146-166210--
1.15eENST0000035006015eENSE00001734789X:153186262-153186080183RHG04_HUMAN167-227610--
1.17ENST0000035006017ENSE00001708678X:153184737-153184609129RHG04_HUMAN228-270430--
1.18dENST0000035006018dENSE00001674126X:153184507-153184286222RHG04_HUMAN271-344740--
1.19bENST0000035006019bENSE00001746827X:153179333-153179232102RHG04_HUMAN345-378340--
1.20bENST0000035006020bENSE00001642653X:153179054-153178863192RHG04_HUMAN379-442640--
1.20gENST0000035006020gENSE00001597003X:153178756-15317867285RHG04_HUMAN443-471290--
1.21ENST0000035006021ENSE00001617221X:153178505-15317847828RHG04_HUMAN471-480100--
1.22aENST0000035006022aENSE00001767059X:153178256-153178154103RHG04_HUMAN480-514350--
1.23ENST0000035006023ENSE00001597291X:153176643-15317658361RHG04_HUMAN515-535210--
1.24bENST0000035006024bENSE00001659670X:153176453-15317637678RHG04_HUMAN535-561270--
1.25bENST0000035006025bENSE00001742632X:153176288-153176154135RHG04_HUMAN561-606460--
1.26aENST0000035006026aENSE00001770031X:153176065-153175960106RHG04_HUMAN606-641360--
1.26dENST0000035006026dENSE00001643104X:153175858-153175625234RHG04_HUMAN641-719790--
1.26eENST0000035006026eENSE00001641277X:153175539-15317546674RHG04_HUMAN719-744261A:739-7468
1.27bENST0000035006027bENSE00002182582X:153175378-153175195184RHG04_HUMAN744-805621A:747-80559
1.28dENST0000035006028dENSE00001737293X:153174989-15317489793RHG04_HUMAN805-836321A:805-81410
1.29ENST0000035006029ENSE00001737862X:153174623-153174524100RHG04_HUMAN836-869340--
1.30eENST0000035006030eENSE00001624831X:153173416-153172831586RHG04_HUMAN870-946770--

(-) 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:76
 aligned with RHG04_HUMAN | P98171 from UniProtKB/Swiss-Prot  Length:946

    Alignment length:91
                                   733       743       753       763       773       783       793       803       813 
          RHG04_HUMAN   724 ESLGADNEPELEAEMPAQEDDLEGVVEAVACFAYTGRTAQELSFRRGDVLRLHERASSDWWRGEHNGMRGLIPHKYITLPAGTEKQVVGAG 814
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2epdA00                A:739-814 SH3 Domains                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........---------------..eeeee...ee.......ee....eeeeeeeee..eeeeee..eeeeee...ee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------SH3  PDB: A:747-805 UniProt: 746-805                        --------- PROSITE
           Transcript 1 (1) Exon 1.26e           ------------------------------------------------------------Exon 1.28d Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.27b  PDB: A:747-805 UniProt: 744-805 [INCOMPLETE]      --------- Transcript 1 (2)
                 2epd A 739 GSSGSSGE---------------GVVEAVACFAYTGRTAQELSFRRGDVLRLHERASSDWWRGEHNGMRGLIPHKYITLPAGTEKQVVGAG 814
                                   | -         -   |   753       763       773       783       793       803       813 
                                 746             747                                                                   

   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  (0, 0)

(no "SCOP Domain" information available for 2EPD)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

NMR Structure(hide GO term definitions)
Chain A   (RHG04_HUMAN | P98171)
molecular function
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0048365    Rac GTPase binding    Interacting selectively and non-covalently with Rac protein, any member of the Rac subfamily of the Ras superfamily of monomeric GTPases.
    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:0005070    SH3/SH2 adaptor activity    Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68).
    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: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).
biological process
    GO:0007266    Rho protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Rho family of proteins switching to a GTP-bound active state.
    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:0030517    negative regulation of axon extension    Any process that stops, prevents, or reduces the frequency, rate or extent of axon outgrowth.
    GO:0030336    negative regulation of cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
    GO:0010764    negative regulation of fibroblast migration    Any process that decreases the rate, frequency or extent of fibroblast cell migration. Fibroblast cell migration is accomplished by extension and retraction of a pseudopodium.
    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: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:0009967    positive regulation of signal transduction    Any process that activates or increases the frequency, rate or extent of signal transduction.
    GO:0051056    regulation of small GTPase mediated signal transduction    Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.
    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: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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    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.

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