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(-) Description

Title :  SOLUTION STRUCTURE OF THE PDZ DOMAIN OF HUMAN RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 11
 
Authors :  K. Inoue, T. Suetake, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  20 Apr 06  (Deposition) - 20 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Pdz Domain, Rho Guanine Nucleotide Exchange Factor 11, Pdz- Rhogef, Arhgef11, Kiaa0380, 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 :  K. Inoue, T. Suetake, F. Hayashi, S. Yokoyama
Solution Structure Of The Pdz Domain Of Human Rho Guanine Nucleotide Exchange Factor 11
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 11
    ChainsA
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050919-12
    Expression System Vector TypePLASMID
    FragmentPDZ DOMAIN
    GeneARHGEF11, KIAA0380
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymPDZ-RHOGEF

 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 2DLS)

(-) Sites  (0, 0)

(no "Site" information available for 2DLS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.ARHGB_HUMAN47-111  1A:11-75

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003614091bENSE00001839709chr1:157014865-157014091775ARHGB_HUMAN1-11110--
1.2ENST000003614092ENSE00001436720chr1:156955965-15695587492ARHGB_HUMAN11-42321A:1-77
1.3ENST000003614093ENSE00000904836chr1:156954229-15695413199ARHGB_HUMAN42-75341A:7-39 (gaps)34
1.4ENST000003614094ENSE00000904837chr1:156950278-15695022950ARHGB_HUMAN75-91171A:39-5517
1.5ENST000003614095ENSE00000904838chr1:156949078-15694902158ARHGB_HUMAN92-111201A:56-7520
1.6ENST000003614096ENSE00000904839chr1:156948174-156947996179ARHGB_HUMAN111-170601A:75-93 (gaps)30
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_HUMAN282-306250--
1.14ENST0000036140914ENSE00000904845chr1:156933096-156932995102ARHGB_HUMAN307-340340--
1.15ENST0000036140915ENSE00001195452chr1:156931567-15693146999ARHGB_HUMAN341-373330--
1.16ENST0000036140916ENSE00000904847chr1:156930252-15693021043ARHGB_HUMAN374-388150--
1.17ENST0000036140917ENSE00000904848chr1:156928934-15692883897ARHGB_HUMAN388-420330--
1.18ENST0000036140918ENSE00000904849chr1:156928656-156928534123ARHGB_HUMAN420-461420--
1.19ENST0000036140919ENSE00001436165chr1:156927607-15692758424ARHGB_HUMAN461-46990--
1.20ENST0000036140920ENSE00001436260chr1:156926356-156926212145ARHGB_HUMAN469-517490--
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

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:93
 aligned with ARHGB_HUMAN | O15085 from UniProtKB/Swiss-Prot  Length:1522

    Alignment length:105
                                    45        55        65        75        85        95       105       115       125       135     
          ARHGB_HUMAN    36 DASETTGLVQRCVIIQKDQHGFGFTVSGDRIVLVQSVRPGGAAMKAGVKEGDRIIKVNGTMVTNSSHLEVVKLIKSGAYVALTLLGSSPSSMGISGLQQDPSPAG 140
               SCOP domains d2dlsa_  A: automated matches                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......-.eeeeeee.......eeee.....eeeee.....hhhh......eeeee..ee....hhhhhhhhhh...eeeeeee...------..----..-.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------PDZ  PDB: A:11-75 UniProt: 47-111                                ----------------------------- PROSITE
           Transcript 1 (1) 1.2    --------------------------------Exon 1.4         Exon 1.5            ----------------------------- Transcript 1 (1)
           Transcript 1 (2) ------Exon 1.3  PDB: A:7-39 (gaps)      -----------------------------------Exon 1.6  PDB: A:75-93 (gaps)  Transcript 1 (2)
                 2dls A   1 GSSGSSG-VQRCVIIQKDQHGFGFTVSGDRIVLVQSVRPGGAAMKAGVKEGDRIIKVNGTMVTNSSHLEVVKLIKSGAYVALTLLGSS------SG----PS-SG  93
                                  | |9        19        29        39        49        59        69        79       | -    ||   -|| | 
                                  7 8                                                                             87     88|   90| | 
                                                                                                                          89    91 | 
                                                                                                                                  92 

   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 2DLS)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

NMR Structure(hide GO term definitions)
Chain A   (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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ARHGB_HUMAN | O150851htj 1xcg 3kz1 3t06 5e6p 5jhg 5jhh 5tyt

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