Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  GTPASE-ACTIVATION DOMAIN FROM RHOGAP
 
Authors :  T. Barrett, B. Xiao, E. J. Dodson, G. Dodson, S. B. Ludbrook, K. Nurmahomed, S. J. Gamblin, A. Musacchio, S. J. Smerdon, J. F. Eccleston
Date :  05 Dec 96  (Deposition) - 15 Oct 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  G-Protein, Gap, Signal-Transduction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Barrett, B. Xiao, E. J. Dodson, G. Dodson, S. B. Ludbrook, K. Nurmahomed, S. J. Gamblin, A. Musacchio, S. J. Smerdon, J. F. Eccleston
The Structure Of The Gtpase-Activating Domain From P50Rhogap.
Nature V. 385 458 1997
PubMed-ID: 9009196  |  Reference-DOI: 10.1038/385458A0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RHOGAP
    Cellular Location: CYTOPLASM
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: GTPASE ACTIVATION DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CDC42 GTPASE-ACTIVATING PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1RGP)

(-) Sites  (0, 0)

(no "Site" information available for 1RGP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049137R369CRHG01_HUMANPolymorphism11822837AR172C

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RHOGAPPS50238 Rho GTPase-activating proteins domain profile.RHG01_HUMAN244-431  1A:47-234

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003119561cENSE00002153911chr11:46722149-4672210149RHG01_HUMAN-00--
1.3aENST000003119563aENSE00002177295chr11:46717706-46717525182RHG01_HUMAN1-45450--
1.4aENST000003119564aENSE00001228762chr11:46717305-4671721096RHG01_HUMAN45-77330--
1.5aENST000003119565aENSE00001228757chr11:46709810-4670972388RHG01_HUMAN77-106300--
1.6ENST000003119566ENSE00001181605chr11:46703732-46703601132RHG01_HUMAN106-150450--
1.7bENST000003119567bENSE00001181598chr11:46702929-4670284387RHG01_HUMAN150-179300--
1.8bENST000003119568bENSE00001181594chr11:46702659-4670256199RHG01_HUMAN179-212340--
1.9ENST000003119569ENSE00001181590chr11:46702297-46702190108RHG01_HUMAN212-248371A:36-5116
1.10ENST0000031195610ENSE00001181585chr11:46702113-4670203777RHG01_HUMAN248-274271A:51-7727
1.11ENST0000031195611ENSE00001181582chr11:46701832-4670175578RHG01_HUMAN274-300271A:77-10327
1.12bENST0000031195612bENSE00001181578chr11:46701326-46701198129RHG01_HUMAN300-343441A:103-14644
1.13ENST0000031195613ENSE00001181574chr11:46701018-46700915104RHG01_HUMAN343-377351A:146-18035
1.14dENST0000031195614dENSE00001181611chr11:46700775-466986302146RHG01_HUMAN378-439621A:181-234 (gaps)54

(-) 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:189
 aligned with RHG01_HUMAN | Q07960 from UniProtKB/Swiss-Prot  Length:439

    Alignment length:199
                                   242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422         
          RHG01_HUMAN   233 PRPPLPNQQFGVSLQHLQEKNPEQEPIPIVLRETVAYLQAHALTTEGIFRRSANTQVVREVQQKYNMGLPVDFDQYNELHLPAVILKTFLRELPEPLLTFDLYPHVVGFLNIDESQRVPATLQVLQTLPEENYQVLRFLTAFLVQISAHSDQNKMTNTNLAVVFGPNLLWAKDAAITLKAINPINTFTKFLLDHQGELF 431
               SCOP domains d1rgpa_ A: p50 RhoGAP domain                                                                                                                                                                            SCOP domains
               CATH domains 1rgpA00 A:36-234 GTPase -GAP domain                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------RhoGAP-1rgpA01 A:63-205                                                                                                                        ----------------------------- Pfam domains
         Sec.struct. author .............hhhhhhh........hhhhhhhhhhhhh.............hhhhhhhhhhhh......hhh....hhhhhhhhhhhhh.......hhhhhhhh......hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..----------.hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------C-------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------RHOGAP  PDB: A:47-234 UniProt: 244-431                                                                                                                                                       PROSITE
           Transcript 1 (1) ---------------Exon 1.10  PDB: A:51-77    -------------------------Exon 1.12b  PDB: A:103-146 UniProt: 300-343 ----------------------------------Exon 1.14d  PDB: A:181-234 (gaps) UniProt: 378-439     Transcript 1 (1)
           Transcript 1 (2) Exon 1.9        -------------------------Exon 1.11  PDB: A:77-103   ------------------------------------------Exon 1.13  PDB: A:146-180          ------------------------------------------------------ Transcript 1 (2)
                 1rgp A  36 PRPPLPNQQFGVSLQHLQEKNPEQEPIPIVLRETVAYLQAHALTTEGIFRRSANTQVVREVQQKYNMGLPVDFDQYNELHLPAVILKTFLRELPEPLLTFDLYPHVVGFLNIDESQRVPATLQVLQTLPEENYQVLRFLTAFLVQISAHSDQNKMTNTNLAVVFGPNLLW----------INPINTFTKFLLDHQGELF 234
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205         -|      225         
                                                                                                                                                                                                   205        216                  

   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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: GAP (15)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RHG01_HUMAN | Q07960)
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:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    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: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:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    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.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1rgp)
 
  Sites
(no "Sites" information available for 1rgp)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1rgp)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1rgp
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RHG01_HUMAN | Q07960
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  RHG01_HUMAN | Q07960
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RHG01_HUMAN | Q07960: 1am4 1grn 1ow3 1tx4 2ngr 5m6x 5m70

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1RGP)