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(-) Description

Title :  SOLUTION STRUCTURE OF THE SAM-DOMAIN OF RHO-GTPASE-ACTIVATING PROTEIN 7
 
Authors :  A. K. Goroncy, M. Sato, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 Apr 06  (Deposition) - 24 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Cell-Free Protein Synthesis, Protein Regulation, 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 :  A. K. Goroncy, M. Sato, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Sam-Domain Of Rho-Gtpase-Activating Protein 7
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RHO-GTPASE-ACTIVATING PROTEIN 7
    ChainsA
    EngineeredYES
    Expression System PlasmidP050207-01
    Expression System Vector TypePLASMID
    FragmentSAM-DOMAIN
    GeneDLC1, ARHGAP7, KIAA1723, STARD12
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymRHO-TYPE GTPASE-ACTIVATING PROTEIN 7, DELETED IN LIVER CANCER 1 PROTEIN, DLC-1, HP PROTEIN, STAR-RELATED LIPID TRANSFER PROTEIN 12, STARD12, START DOMAIN- CONTAINING PROTEIN 12

 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 2DKY)

(-) Sites  (0, 0)

(no "Site" information available for 2DKY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Phe A:47 -Pro A:48

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DKY)

(-) Exons   (7, 7)

NMR Structure (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000002762972bENSE00001189213chr8:13372395-13372111285RHG07_HUMAN-00--
1.3bENST000002762973bENSE00001388926chr8:13357705-133565581148RHG07_HUMAN1-3413410--
1.4ENST000002762974ENSE00000979612chr8:13259128-13258979150RHG07_HUMAN342-391501A:1-22
1.5bENST000002762975bENSE00001015479chr8:13251202-13251062141RHG07_HUMAN392-438471A:3-16 (gaps)44
1.6aENST000002762976aENSE00001087081chr8:13162811-1316277834RHG07_HUMAN439-450121A:17-20 (gaps)12
1.12ENST0000027629712ENSE00001189219chr8:12973166-1297309572RHG07_HUMAN450-474251A:20-4425
1.13ENST0000027629713ENSE00001087061chr8:12968332-1296825182RHG07_HUMAN474-501281A:44-7128
1.14ENST0000027629714ENSE00001087065chr8:12960362-1296029964RHG07_HUMAN501-522221A:71-8616
1.15eENST0000027629715eENSE00001087057chr8:12958279-129568561424RHG07_HUMAN523-9974751A:87-915
1.16ENST0000027629716ENSE00001087059chr8:12956084-12955908177RHG07_HUMAN997-1056600--
1.18ENST0000027629718ENSE00001087055chr8:12952754-12952595160RHG07_HUMAN1056-1109540--
1.19cENST0000027629719cENSE00001087071chr8:12952466-12952268199RHG07_HUMAN1110-1176670--
1.20ENST0000027629720ENSE00001087051chr8:12950334-12950121214RHG07_HUMAN1176-1247720--
1.21ENST0000027629721ENSE00001087050chr8:12948941-12948827115RHG07_HUMAN1247-1285390--
1.22ENST0000027629722ENSE00001087069chr8:12947979-12947761219RHG07_HUMAN1286-1358730--
1.23bENST0000027629723bENSE00001087054chr8:12946213-12945996218RHG07_HUMAN1359-1431730--
1.24aENST0000027629724aENSE00001087052chr8:12943972-12943799174RHG07_HUMAN1431-1489590--
1.25eENST0000027629725eENSE00001216909chr8:12943440-129408702571RHG07_HUMAN1489-1528400--

(-) 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:91
 aligned with RHG07_HUMAN | Q96QB1 from UniProtKB/Swiss-Prot  Length:1528

    Alignment length:199
                                   390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570         
          RHG07_HUMAN   381 GTPTNLRRHVPDLESGSESGADTISVNQTRVNLSSDTESTDLPSSTPVANSGTKPKTTAIQGISEKEKAEIEAKEACDWLRATGFPQYAQLYEDFLFPIDISLVKREHDFLDRDAIEALCRRLNTLNKCAVMKLEISPHRKRSDDSDEDEPCAISGKWTFQRDSKRWSRLEEFDVFSPKQDLVPGSPDDSHPKDGPSPG 579
               SCOP domains --------------------d2dk                             ya1 A:8-        85 Deleted in liver cancer 1 protein, DLC-1                       ---------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------------...-......-----------------------------...hhhhh--------hhhhhhhhhhhhhhh..hhhhhhhh.....hhhhhhhhh...hhhhhhhhhhhhhhhhhhh......----------------------------------------------------------..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4   Exon 1.5b  PDB: A:3-16 (gaps) UniProt: 392-438 -----------Exon 1.12  PDB: A:20-44  --------------------------Exon 1.14  PDB: A:71-8Exon 1.15e  PDB: A:87-91 UniProt: 523-997 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.6a   -----------------------Exon 1.13  PDB: A:44-71     ------------------------------------------------------------------------------ Transcript 1 (2)
                 2dky A   1 GS------------SGS-SGMCRK-----------------------------KPDTMILT--------QIEAKEACDWLRATGFPQYAQLYEDFLFPIDISLVKREHDFLDRDAIEALCRRLNTLNKCAVMKLES----------------------------------------------------------GPSSG  91
                             |       -    | | |7   |     -         -         -   |    18|       20        30        40        50        60        70        80     |   -         -         -         -         -         -    |    
                             2            3 5 6   11                            12     19       20                                                                86                                                         87    

   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 2DKY)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

NMR Structure(hide GO term definitions)
Chain A   (RHG07_HUMAN | Q96QB1)
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:0042169    SH2 domain binding    Interacting selectively and non-covalently with a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    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: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:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0048041    focal adhesion assembly    The aggregation and bonding together of a set of components to form a focal adhesion, a complex of intracellular signaling and structural proteins that provides a structural link between the internal actin cytoskeleton and the ECM, and also function as a locus of signal transduction activity.
    GO:0030900    forebrain development    The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    GO:0003007    heart morphogenesis    The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0021575    hindbrain morphogenesis    The process in which the anatomical structure of the hindbrain is generated and organized. The hindbrain is the region consisting of the medulla, pons and cerebellum. Areas of the hindbrain control motor and autonomic functions.
    GO:0035024    negative regulation of Rho protein signal transduction    Any process that stops, prevents, or reduces the frequency, rate or extent of Rho protein signal transduction.
    GO:0030336    negative regulation of cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0051895    negative regulation of focal adhesion assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of focal adhesion assembly, the establishment and maturation of focal adhesions.
    GO:0051497    negative regulation of stress fiber assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of the assembly a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts.
    GO:0001843    neural tube closure    The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:1900119    positive regulation of execution phase of apoptosis    Any process that activates or increases the frequency, rate or extent of execution phase of apoptosis.
    GO:0035307    positive regulation of protein dephosphorylation    Any process that activates or increases the frequency, rate or extent of removal of phosphate groups from a protein.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
    GO:0032956    regulation of actin cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    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.
    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:0005901    caveola    A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0030864    cortical actin cytoskeleton    The portion of the actin cytoskeleton, comprising filamentous actin and associated proteins, that lies just beneath the plasma membrane.
    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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RHG07_HUMAN | Q96QB12gyt 2kap 2loz 3kuq 5fzt

(-) Related Entries Specified in the PDB File

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