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(-) Description

Authors :  Y. Tong, M. Buck
Date :  11 May 07  (Deposition) - 18 Mar 08  (Release) - 24 Feb 09  (Revision)
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Protein, Ubiquitin Fold, Signaling Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  Y. Tong, P. K. Hota, M. B. Hamaneh, M. Buck
Insights Into Oncogenic Mutations Of Plexin-B1 Based On The Solution Structure Of The Rho Gtpase Binding Domain
Structure V. 16 246 2008
PubMed-ID: 18275816  |  Reference-DOI: 10.1016/J.STR.2007.12.012
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLEXIN-B1
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System VectorPET11A
    Expression System Vector TypeVECTOR
    GenePLXNB1, KIAA0407, SEP
    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 2JPH)

(-) Sites  (0, 0)

(no "Site" information available for 2JPH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2JPH)

(-) Exons   (4, 4)

NMR Structure (4, 4)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength

(-) 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:122
 aligned with PLXB1_HUMAN | O43157 from UniProtKB/Swiss-Prot  Length:2135

    Alignment length:122
                                  1750      1760      1770      1780      1790      1800      1810      1820      1830      1840      1850      1860  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --Plexin_cytopl-2jphA01 A:3-122                                                                                            Pfam domains
         Sec.struct. author ........eeeee.............eeeee....hhhhhhhhhhhh................eeeee.....eeee.................hhhhhh....eeeeee............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.26c    Exon 1.27b  PDB: A:10-66 UniProt: 1750-1806              ----------------------------------Exon 1.28a             Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------Exon 1.27d  PDB: A:66-100          ---------------------- Transcript 1 (2)
                                    10        20        30        40        50        60        70        80        90       100       110       120  

   Legend:   → Mismatch (orange background)
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    → 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 2JPH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JPH)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (32, 32)

NMR Structure(hide GO term definitions)
Chain A   (PLXB1_HUMAN | O43157)
molecular function
    GO:0032794    GTPase activating protein binding    Interacting selectively and non-covalently with a GTPase activating protein.
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    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:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0017154    semaphorin receptor activity    Combining with a semaphorin, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    GO:0030215    semaphorin receptor binding    Interacting selectively and non-covalently with semaphorin receptors.
    GO:0004888    transmembrane signaling receptor activity    Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
biological process
    GO:0048675    axon extension    Long distance growth of a single axon process involved in cellular development.
    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: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:0007162    negative regulation of cell adhesion    Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
    GO:0033689    negative regulation of osteoblast proliferation    Any process that stops, prevents or reduces the rate or extent of osteoblast proliferation.
    GO:0048812    neuron projection morphogenesis    The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites.
    GO:0043931    ossification involved in bone maturation    The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone, involved in the progression of the skeleton 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:0050772    positive regulation of axonogenesis    Any process that activates or increases the frequency, rate or extent of axonogenesis.
    GO:0014068    positive regulation of phosphatidylinositol 3-kinase signaling    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:0043087    regulation of GTPase activity    Any process that modulates the rate of GTP hydrolysis by a GTPase.
    GO:0030334    regulation of cell migration    Any process that modulates the frequency, rate or extent of cell migration.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0051493    regulation of cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:0071526    semaphorin-plexin signaling pathway    A series of molecular signals generated as a consequence of a semaphorin receptor (composed of a plexin and a neurophilin) binding to a semaphorin ligand.
    GO:1902287    semaphorin-plexin signaling pathway involved in axon guidance    Any semaphorin-plexin signaling pathway that is involved in axon guidance.
    GO:1900220    semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis    Any semaphorin-plexin signaling pathway that contributes to bone trabecula morphogenesis.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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.
    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:0002116    semaphorin receptor complex    A stable binary complex of a neurophilin and a plexin, together forming a functional semaphorin receptor.


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 Related Entries

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

        PLXB1_HUMAN | O431572os6 2r2o 2rex 3hm6 3ol2 3su8 3sua 5b4w

(-) Related Entries Specified in the PDB File