Show PDB file:   
         Plain Text   HTML   (compressed file size)
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Authors :  Y. Wu, A. Ghosh, R. Shastry, J. Hua, C. Ciccosanti, Q. Zhang, M. Jiang, G. Swapna, T. Acton, R. Xiao, J. Everett, G. Montelione, T. Szyperski, Northeast Structural Genomics Consortium (Nesg)
Date :  16 Mar 09  (Deposition) - 31 Mar 09  (Release) - 31 Mar 09  (Revision)
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Structure, Alternative Splicing, Calcium, Cell Junction, Cell Projection, Coiled Coil, Endocytosis, Membrane, Phosphoprotein, Sh3 Domain, Synapse, Synaptosome, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  Y. Wu, A. Ghosh, R. Shastry, J. Hua, C. Ciccosanti, Q. Zhang, M. Jiang, G. Swapna, T. Acton, R. Xiao, J. Everett, G. Montelione, T. Szyperski
Solution Structure Of Protein Itsn1 From Homo Sapiens. Northeast Structural Genomics Consortium Target Hr5524A
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTERSECTIN-1
    Expression SystemESCHERICHIA COLI
    Expression System Cell LineBL21(DE3)+ MAGIC
    Expression System Taxid562
    FragmentRESIDUES 210-312
    GeneITSN1, ITSN, SH3D1A
    Organism CommonMAN
    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 2KGR)

(-) Sites  (0, 0)

(no "Site" information available for 2KGR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

NMR Structure (3, 3)
1EHPS50031 EH domain profile.ITSN1_HUMAN21-100
2EF_HAND_2PS50222 EF-hand calcium-binding domain profile.ITSN1_HUMAN53-88
3EF_HAND_1PS00018 EF-hand calcium-binding domain.ITSN1_HUMAN66-78

(-) Exons   (4, 4)

NMR Structure (4, 4)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.17ENST0000038131817ENSE00001758830chr21:35140017-35140132116ITSN1_HUMAN309-348401A:100-111 (gaps)34

(-) 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:111
 aligned with ITSN1_HUMAN | Q15811 from UniProtKB/Swiss-Prot  Length:1721

    Alignment length:133
                                   219       229       239       249       259       269       279       289       299       309       319       329       339   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh.......eeehhhhhhhhhh...hhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhh........hhhhh........----------------------........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------EH  PDB: A:12-101 UniProt: 221-310                                                        -------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------EF_HAND_2  PDB: A:45-80             ----------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------EF_HAND_1    --------------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.13  PDB: A:1-33           --------------------Exon 1.16  PDB: A:54-100 UniProt: 263-309      --------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------Exon 1.15  PDB: A:33-5---------------------------------------------Exon 1.17  PDB: A:100-111 (gaps)   Transcript 1 (2)
                                    10        20        30        40        50        60        70        80        90       100  |      -         -     | 108   
                                                                                                                                103                    104       

   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 2KGR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (31, 31)

NMR Structure(hide GO term definitions)
Chain A   (ITSN1_HUMAN | Q15811)
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:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0019209    kinase activator activity    Binds to and increases the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0070064    proline-rich region binding    Interacting selectively and non-covalently with a proline-rich region, i.e. a region that contains a high proportion of proline residues, in a protein.
    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:0032947    protein complex scaffold activity    A structural molecule activity that provides a physical support for the assembly of a multiprotein complex. The scaffold may or may not be part of the final complex.
biological process
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    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:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
    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:0042327    positive regulation of phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
    GO:0051897    positive regulation of protein kinase B signaling    Any process that activates or increases the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    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:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
    GO:0048488    synaptic vesicle endocytosis    Clathrin-mediated endocytosis of presynaptic membrane that recycles synaptic vesicle membrane and its components following synaptic vesicle exocytosis. This process starts with coating of the membrane with adaptor proteins and clathrin prior to invagination and ends when uncoating has finished.
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:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005905    clathrin-coated pit    A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes.
    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:0030139    endocytic vesicle    A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
    GO:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.


(-) Interactive Views

NMR Structure
  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)
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
(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
(no "Ligands, Modified Residues, Ions" information available for 2kgr)
(no "Sites" information available for 2kgr)
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2kgr)

(-) Still Images

  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
    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
  ITSN1_HUMAN | Q15811
    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
  ITSN1_HUMAN | Q15811
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

        ITSN1_HUMAN | Q158111ki1 2khn 3fia 3qbv 4iim 5hzi 5hzj 5hzk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2KGR)