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(-) Description

Title :  DBL HOMOLOGY DOMAIN FROM BETA-PIX
 
Authors :  B. Aghazadeh, K. Zhu, T. J. Kubiseski, G. A. Liu, T. Pawson, Y. Zheng, M. K. Rosen
Date :  22 Oct 98  (Deposition) - 24 Oct 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Rho-Gtpase Exchange Factor, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Aghazadeh, K. Zhu, T. J. Kubiseski, G. A. Liu, T. Pawson, Y. Zheng, M. K. Rosen
Structure And Mutagenesis Of The Dbl Homology Domain
Nat. Struct. Biol. V. 5 1098 1998
PubMed-ID: 9846881  |  Reference-DOI: 10.1038/4209
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (PIX)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET11A
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    FragmentDBL HOMOLOGY DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 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 1BY1)

(-) Sites  (0, 0)

(no "Site" information available for 1BY1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BY1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BY1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BY1)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DH_2PS50010 Dbl homology (DH) domain profile.ARHG7_HUMAN271-451  1A:13-193
2DH_1PS00741 Dbl homology (DH) domain signature.ARHG7_HUMAN399-424  1A:141-166

(-) Exons   (7, 7)

NMR Structure (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003757411cENSE00001666787chr13:111767624-111768038415ARHG7_HUMAN1-55550--
1.2gENST000003757412gENSE00001805811chr13:111806252-11180633887ARHG7_HUMAN56-84290--
1.3ENST000003757413ENSE00001468253chr13:111811374-11181143663ARHG7_HUMAN85-105210--
1.7ENST000003757417ENSE00001735504chr13:111857636-11185772085ARHG7_HUMAN106-134290--
1.9ENST000003757419ENSE00001732485chr13:111862219-111862349131ARHG7_HUMAN134-177440--
1.10cENST0000037574110cENSE00001759601chr13:111870026-111870227202ARHG7_HUMAN178-245680--
1.11ENST0000037574111ENSE00001733623chr13:111885552-11188564089ARHG7_HUMAN245-274301A:1-1616
1.13ENST0000037574113ENSE00001676059chr13:111896219-11189631395ARHG7_HUMAN275-306321A:17-4832
1.14ENST0000037574114ENSE00001669520chr13:111896546-11189664196ARHG7_HUMAN306-338331A:48-8033
1.17ENST0000037574117ENSE00001799183chr13:111919895-111920017123ARHG7_HUMAN338-379421A:80-12142
1.18ENST0000037574118ENSE00001767862chr13:111926161-111926299139ARHG7_HUMAN379-425471A:121-16747
1.19ENST0000037574119ENSE00001800550chr13:111927078-11192713760ARHG7_HUMAN426-445201A:168-18720
1.20aENST0000037574120aENSE00001705581chr13:111927879-111928025147ARHG7_HUMAN446-494491A:188-20922
1.21ENST0000037574121ENSE00001641405chr13:111929934-11193002087ARHG7_HUMAN495-523290--
1.22ENST0000037574122ENSE00001742777chr13:111932619-11193269779ARHG7_HUMAN524-550270--
1.23ENST0000037574123ENSE00001643717chr13:111932885-111933024140ARHG7_HUMAN550-596470--
1.25dENST0000037574125dENSE00000686825chr13:111935486-111935710225ARHG7_HUMAN597-671750--
1.26bENST0000037574126bENSE00000686829chr13:111938494-11193858794ARHG7_HUMAN672-703320--
1.27ENST0000037574127ENSE00000686833chr13:111940701-11194079090ARHG7_HUMAN703-733310--
1.28fENST0000037574128fENSE00001237026chr13:111944465-1119475423078ARHG7_HUMAN733-803710--

(-) 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:209
 aligned with ARHG7_HUMAN | Q14155 from UniProtKB/Swiss-Prot  Length:803

    Alignment length:209
                                   268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458         
          ARHG7_HUMAN   259 PKGFDTTAINKSYYNVVLQNILETENEYSKELQTVLSTYLRPLQTSEKLSSANISYLMGNLEEICSFQQMLVQSLEECTKLPEAQQRVGGCFLNLMPQMKTLYLTYCANHPSAVNVLTEHSEELGEFMETKGASSPGILVLTTGLSKPFMRLDKYPTLLKELERHMEDYHTDRQDIQKSMAAFKNLSAQCQEVRKRKELELQILTEAIR 467
               SCOP domains d1by1a_ A: beta-pix                                                                                                                                                                                               SCOP domains
               CATH domains 1by1A00 A:1-209 Dbl Homology Domain; Chain A                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhh.hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhh............hhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------DH_2  PDB: A:13-193 UniProt: 271-451                                                                                                                                                 ---------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------DH_1  PDB: A:141-166      ------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.11       Exon 1.13  PDB: A:17-48         -------------------------------Exon 1.17  PDB: A:80-121 UniProt: 338-379 ----------------------------------------------Exon 1.19           Exon 1.20a             Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.14  PDB: A:48-80          ----------------------------------------Exon 1.18  PDB: A:121-167 UniProt: 379-425     ------------------------------------------ Transcript 1 (2)
                 1by1 A   1 MKGFDTTAINKSYYNVVLQNILETENEYSKELQTVLSTYLRPLQTSEKLSSANISYLMGNLEEICSFQQMLVQSLEECTKLPEAQQRVGGCFLNLMPQMKTLYLTYCANHPSAVNVLTEHSEELGEFMETKGASSPGILVLTTGLSKPFMRLDKYPTLLKELERHMEDYHTDRQDIQKSMAAFKNLSAQCQEVRKRKELELQILTEAIR 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         

   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  (1, 1)

NMR Structure

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BY1)

(-) Gene Ontology  (36, 36)

NMR Structure(hide GO term definitions)
Chain A   (ARHG7_HUMAN | Q14155)
molecular function
    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).
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
    GO:0007030    Golgi organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus.
    GO:0048013    ephrin receptor signaling pathway    The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
    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:0002244    hematopoietic progenitor cell differentiation    The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0030032    lamellipodium assembly    Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
    GO:0042059    negative regulation of epidermal growth factor receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
    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:0010763    positive regulation of fibroblast migration    Any process that increases the rate, frequency or extent of fibroblast cell migration. Fibroblast cell migration is accomplished by extension and retraction of a pseudopodium.
    GO:0060124    positive regulation of growth hormone secretion    Any process that increases the frequency, rate or extent of the regulated release of growth hormone from a cell.
    GO:2000394    positive regulation of lamellipodium morphogenesis    Any process that activates or increases the frequency, rate or extent of lamellipodium morphogenesis.
    GO:0032092    positive regulation of protein binding    Any process that activates or increases the frequency, rate or extent of protein binding.
    GO:1900026    positive regulation of substrate adhesion-dependent cell spreading    Any process that activates or increases the frequency, rate or extent of substrate adhesion-dependent cell spreading.
    GO:1904424    regulation of GTP binding    Any process that modulates the frequency, rate or extent of GTP binding.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein 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:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    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:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    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:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.
    GO:0000322    storage vacuole    A vacuole that functions primarily in the storage of materials, including nutrients, pigments, waste products, and small molecules.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ARHG7_HUMAN | Q141551zsg 2l3g 5sxp

(-) Related Entries Specified in the PDB File

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