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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TIAM1 PHCCEX DOMAIN
 
Authors :  S. Terawaki, K. Kitano, T. Mori, Y. Zhai, Y. Higuchi, N. Itoh, T. Watanabe, K. Kaibuchi, T. Hakoshima
Date :  07 Oct 09  (Deposition) - 24 Nov 09  (Release) - 19 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Guanine Nucleotide Exchange Factor, Guanine-Nucleotide Releasing Factor, Lipoprotein, Myristate, Phosphoprotein, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Terawaki, K. Kitano, T. Mori, Y. Zhai, Y. Higuchi, N. Itoh, T. Watanabe, K. Kaibuchi, T. Hakoshima
The Phccex Domain Of Tiam1/2 Is A Novel Protein- And Membrane-Binding Module
Embo J. V. 29 236 2010
PubMed-ID: 19893486  |  Reference-DOI: 10.1038/EMBOJ.2009.323
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - T-LYMPHOMA INVASION AND METASTASIS-INDUCING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX6P-3
    Expression System StrainBL21RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentPHCCEX DOMAIN, RESIDUES 429-702
    GeneTIAM1, TIAM-1
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymTIAM-1

 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 3A8N)

(-) Sites  (0, 0)

(no "Site" information available for 3A8N)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A8N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3A8N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A8N)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.TIAM1_MOUSE439-547  1A:439-547

(-) Exons   (0, 0)

(no "Exon" information available for 3A8N)

(-) 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:230
 aligned with TIAM1_MOUSE | Q60610 from UniProtKB/Swiss-Prot  Length:1591

    Alignment length:238
                                   442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662        
          TIAM1_MOUSE   433 TVRKAGALAVKNFLVHKKNKKVESATRRKWKHYWVSLKGCTLFFYETDGRSGIDHNSVPKHAVWVENSIVQAVPEHPKKDFVFCLSNSLGDAFLFQTTSQTELENWITAIHSACAAAVARHHHKEDTLRLLKSEIKKLEQKIDMDEKMKKMGEMQLSSVTDSKKKKTILDQIFVWEQNLEQFQMDLFRFRCYLASLQGGELPNPKRLLAFASRPTKVAMGRLGIFSVSSFHALVAART 670
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeeee...eee.......eeeeeeee..ee......--------............ee..............eee...eeee....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh.hhhhhhhh........hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------PH_DOMAIN  PDB: A:439-547 UniProt: 439-547                                                                   --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a8n A 433 TVRKAGALAVKNFLVHKKNKKVESATRRKWKHYWVSLKGCTLFFYETD--------SVPKHAVWVENSIVQAVPEHPKKDFVFCLSNSLGDAFLFQTTSQTELENWITAIHSACAAAVARHHHKEDTLRLLKSEIKKLEQKIDMDEKMKKMGEMQLSSVTDSKKKKTILDQIFVWEQNLEQFQMDLFRFRCYLASLQGGELPNPKRLLAFASRPTKVAMGRLGIFSVSSFHALVAART 670
                                   442       452       462       472       | -      |492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662        
                                                                         480      489                                                                                                                                                                                     

   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  (0, 0)

(no "SCOP Domain" information available for 3A8N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3A8N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A8N)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TIAM1_MOUSE | Q60610)
molecular function
    GO:0030676    Rac guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rac 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: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:0046875    ephrin receptor binding    Interacting selectively and non-covalently with an ephrin receptor.
    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:0019900    kinase binding    Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    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:0030971    receptor tyrosine kinase binding    Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity.
    GO:0005057    signal transducer activity, downstream of receptor    Conveys a signal from an upstream receptor or intracellular signal transducer, converting the signal into a form where it can ultimately trigger a change in the state or activity of a cell.
biological process
    GO:0016601    Rac protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Rac family of proteins switching to a GTP-bound active state.
    GO:0090630    activation of GTPase activity    Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP.
    GO:0031547    brain-derived neurotrophic factor receptor signaling pathway    The series of molecular signals generated as a consequence of a brain-derived neurotrophic factor receptor binding to one of its physiological ligands.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0007160    cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules.
    GO:0048013    ephrin receptor signaling pathway    The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
    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:0050772    positive regulation of axonogenesis    Any process that activates or increases the frequency, rate or extent of axonogenesis.
    GO:0010976    positive regulation of neuron projection development    Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0032092    positive regulation of protein binding    Any process that activates or increases the frequency, rate or extent of protein binding.
    GO:0043087    regulation of GTPase activity    Any process that modulates the rate of GTP hydrolysis by a GTPase.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
    GO:1904338    regulation of dopaminergic neuron differentiation    Any process that modulates the frequency, rate or extent of dopaminergic neuron differentiation.
    GO:2000050    regulation of non-canonical Wnt signaling pathway    Any process that modulates the frequency, rate or extent of non-canonical Wnt signaling pathway.
    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: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:0044291    cell-cell contact zone    Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions, e.g., the intercalated disk of muscle.
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    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:0031234    extrinsic component of cytoplasmic side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TIAM1_MOUSE | Q606101foe

(-) Related Entries Specified in the PDB File

3a8p TIAM2 PHCCEX DOMAIN
3a8q TIAM2 PHCCEX DOMAIN AT LOW RESOLUTION