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

(-) Description

Title :  STRUCTURE OF THE RGS-LIKE DOMAIN FROM PDZ-RHOGEF
 
Authors :  K. L. Longenecker, M. E. Lewis, H. Chikumi, J. S. Gutkind, Z. S. Derewenda
Date :  29 Dec 00  (Deposition) - 11 Jul 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  F
Keywords :  Rgs-Like, Regulator Of G Protein Signaling, Gef, Guanine Nucleotide Exchange Factor, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. L. Longenecker, M. E. Lewis, H. Chikumi, J. S. Gutkind, Z. S. Derewenda
Structure Of The Rgs-Like Domain From Pdz-Rhogef: Linking Heterotrimeric G Protein-Coupled Signaling To Rho Gtpases.
Structure V. 9 559 2001
PubMed-ID: 11470431  |  Reference-DOI: 10.1016/S0969-2126(01)00620-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KIAA0380
    ChainsF
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHIS-PARALLEL
    Expression System StrainB834(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRGS-LIKE DOMAIN (RESIDUES 281-490)
    GeneKIAA0380
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1HTJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HTJ)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RGSPS50132 RGS domain profile.ARHGB_HUMAN313-419  1F:313-419

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003614091bENSE00001839709chr1:157014865-157014091775ARHGB_HUMAN1-11110--
1.2ENST000003614092ENSE00001436720chr1:156955965-15695587492ARHGB_HUMAN11-42320--
1.3ENST000003614093ENSE00000904836chr1:156954229-15695413199ARHGB_HUMAN42-75340--
1.4ENST000003614094ENSE00000904837chr1:156950278-15695022950ARHGB_HUMAN75-91170--
1.5ENST000003614095ENSE00000904838chr1:156949078-15694902158ARHGB_HUMAN92-111200--
1.6ENST000003614096ENSE00000904839chr1:156948174-156947996179ARHGB_HUMAN111-170600--
1.7ENST000003614097ENSE00000904840chr1:156946846-15694677572ARHGB_HUMAN171-194240--
1.9ENST000003614099ENSE00000904841chr1:156939835-15693979046ARHGB_HUMAN195-210160--
1.10ENST0000036140910ENSE00000904842chr1:156939150-15693907477ARHGB_HUMAN210-235260--
1.11aENST0000036140911aENSE00000904843chr1:156937916-156937779138ARHGB_HUMAN236-281460--
1.13ENST0000036140913ENSE00000904844chr1:156933386-15693331275ARHGB_HUMAN282-306251F:306-3061
1.14ENST0000036140914ENSE00000904845chr1:156933096-156932995102ARHGB_HUMAN307-340341F:307-34034
1.15ENST0000036140915ENSE00001195452chr1:156931567-15693146999ARHGB_HUMAN341-373331F:341-37333
1.16ENST0000036140916ENSE00000904847chr1:156930252-15693021043ARHGB_HUMAN374-388151F:374-38815
1.17ENST0000036140917ENSE00000904848chr1:156928934-15692883897ARHGB_HUMAN388-420331F:388-42033
1.18ENST0000036140918ENSE00000904849chr1:156928656-156928534123ARHGB_HUMAN420-461421F:420-46142
1.19ENST0000036140919ENSE00001436165chr1:156927607-15692758424ARHGB_HUMAN461-46991F:461-4699
1.20ENST0000036140920ENSE00001436260chr1:156926356-156926212145ARHGB_HUMAN469-517491F:469-48719
1.21bENST0000036140921bENSE00001074420chr1:156925591-15692549597ARHGB_HUMAN518-550330--
1.22ENST0000036140922ENSE00001195422chr1:156924713-15692468430ARHGB_HUMAN550-560110--
1.23ENST0000036140923ENSE00001054866chr1:156921491-156921365127ARHGB_HUMAN560-602430--
1.24ENST0000036140924ENSE00000904853chr1:156918290-156918111180ARHGB_HUMAN602-662610--
1.25ENST0000036140925ENSE00001195407chr1:156918020-15691797348ARHGB_HUMAN662-678170--
1.26ENST0000036140926ENSE00000904855chr1:156917748-156917561188ARHGB_HUMAN678-741640--
1.27aENST0000036140927aENSE00000904856chr1:156917242-156917096147ARHGB_HUMAN741-790500--
1.28ENST0000036140928ENSE00000904857chr1:156916807-15691672880ARHGB_HUMAN790-816270--
1.29ENST0000036140929ENSE00000904858chr1:156916579-156916454126ARHGB_HUMAN817-858420--
1.30aENST0000036140930aENSE00000904859chr1:156915954-156915837118ARHGB_HUMAN859-898400--
1.31bENST0000036140931bENSE00001253778chr1:156914989-156914811179ARHGB_HUMAN898-957600--
1.32ENST0000036140932ENSE00001195373chr1:156914225-15691415076ARHGB_HUMAN958-983260--
1.33ENST0000036140933ENSE00000904862chr1:156913894-156913727168ARHGB_HUMAN983-1039570--
1.34ENST0000036140934ENSE00000904863chr1:156912572-15691248291ARHGB_HUMAN1039-1069310--
1.35ENST0000036140935ENSE00000904864chr1:156911781-156911656126ARHGB_HUMAN1069-1111430--
1.36ENST0000036140936ENSE00000904865chr1:156911225-15691116462ARHGB_HUMAN1111-1132220--
1.37aENST0000036140937aENSE00000904866chr1:156910217-156909999219ARHGB_HUMAN1132-1205740--
1.37cENST0000036140937cENSE00001253771chr1:156909702-156909340363ARHGB_HUMAN1205-13261220--
1.37fENST0000036140937fENSE00001195338chr1:156908305-15690821096ARHGB_HUMAN1326-1358330--
1.38ENST0000036140938ENSE00001253710chr1:156907288-156907041248ARHGB_HUMAN1358-1440830--
1.39ENST0000036140939ENSE00000904870chr1:156906797-156906608190ARHGB_HUMAN1441-1504640--
1.40aENST0000036140940aENSE00001847612chr1:156905850-156905316535ARHGB_HUMAN1504-1522190--

(-) 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 F from PDB  Type:PROTEIN  Length:182
 aligned with ARHGB_HUMAN | O15085 from UniProtKB/Swiss-Prot  Length:1522

    Alignment length:182
                                   315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485  
          ARHGB_HUMAN   306 ESDIIFQDLEKLKSRPAHLGVFLRYIFSQADPSPLLFYLCAEVYQQASPKDSRSLGKDIWNIFLEKNAPLRVKIPEMLQAEIDSRLRNSEDARGVLCEAQEAAMPEIQEQIHDYRTKRTLGLGSLYGENDLLDLDGDPLRERQVAEKQLAALGDILSKYEEDRSAPMDFALNTYMSHAGIRL 487
               SCOP domains d1htjf_ F: Pdz-RhoGEF RGS-like domain                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------RGS  PDB: F:313-419 UniProt: 313-419                                                                       -------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1Exon 1.14  PDB: F:307-340         Exon 1.15  PDB: F:341-373        Exon 1.16      -------------------------------Exon 1.18  PDB: F:420-461 UniProt: 420-461-------Exon 1.20           Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------Exon 1.17  PDB: F:388-420        ----------------------------------------Exon 1.19------------------ Transcript 1 (2)
                 1htj F 306 ESDIIFQDLEKLKSRPAHLGVFLRYIFSQADPSPLLFYLCAEVYQQASPKDSRSLGKDIWNIFLEKNAPLRVKIPEmLQAEIDSRLRNSEDARGVLCEAQEAAmPEIQEQIHDYRTKRTLGLGSLYGENDLLDLDGDPLRERQVAEKQLAALGDILSAYAADRSAPmDFALNTYmSHAGIRL 487
                                   315       325       335       345       355       365       375      |385       395       405   |   415       425       435       445       455       465      |475    |  485  
                                                                                                      382-MSE                    409-MSE                                                        472-MSE 480-MSE   

   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  (0, 0)

(no "CATH Domain" information available for 1HTJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HTJ)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain F   (ARHGB_HUMAN | O15085)
molecular function
    GO:0001664    G-protein coupled receptor binding    Interacting selectively and non-covalently with a G-protein coupled receptor.
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    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: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:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    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: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:0000910    cytokinesis    The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.
    GO:0030010    establishment of cell polarity    The specification and formation of anisotropic intracellular organization or cell growth patterns.
    GO:0006928    movement of cell or subcellular component    The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
    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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
    GO:0001558    regulation of cell growth    Any process that modulates the frequency, rate, extent or direction of cell growth.
    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:0006941    striated muscle contraction    A process in which force is generated within striated muscle tissue, resulting in the shortening of the muscle. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Striated muscle is a type of muscle in which the repeating units (sarcomeres) of the contractile myofibrils are arranged in registry throughout the cell, resulting in transverse or oblique striations observable at the level of the light microscope.
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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1htj)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1htj)
 

(-) 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
  1htj
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ARHGB_HUMAN | O15085
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  ARHGB_HUMAN | O15085
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ARHGB_HUMAN | O150851xcg 2dls 3kz1 3t06 5e6p 5jhg 5jhh 5tyt

(-) Related Entries Specified in the PDB File

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