Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
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

Title :  CT10-REGULATED KINASE ISOFORM I
 
Authors :  Y. Kobashigawa, S. Tanaka, F. Inagaki
Date :  10 Nov 05  (Deposition) - 10 Nov 06  (Release) - 08 Jul 08  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Sh2, Sh3, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Kobashigawa, M. Sakai, M. Naito, M. Yokochi, H. Kumeta, Y. Makino, K. Ogura, S. Tanaka, F. Inagaki
Structural Basis For The Transforming Activity Of Human Cancer-Related Signaling Adaptor Protein Crk.
Nat. Struct. Mol. Biol. V. 14 503 2007
PubMed-ID: 17515907  |  Reference-DOI: 10.1038/NSMB1241
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - V-CRK SARCOMA VIRUS CT10 ONCOGENE HOMOLOG ISOFORM A
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPPRO EX-HTB
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentISOFORM I
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCT10-REGULATED KINASE

 Structural Features

(-) Chains, Units

  
NMR Structure 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2EYY)

(-) Sites  (0, 0)

(no "Site" information available for 2EYY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.CRK_HUMAN13-118  1A:13-118
2SH3PS50002 Src homology 3 (SH3) domain profile.CRK_HUMAN132-192  1A:132-192

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003005741aENSE00001199129chr17:1359552-1359171382CRK_HUMAN1-81811A:1-8181
1.2bENST000003005742bENSE00001199117chr17:1340449-1339914536CRK_HUMAN81-2591791A:81-204124
1.3bENST000003005743bENSE00001820839chr17:1326944-13239832962CRK_HUMAN260-304450--

(-) 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:204
 aligned with CRK_HUMAN | P46108 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    
            CRK_HUMAN     1 MAGNFDSEERSSWYWGRLSRQEAVALLQGQRHGVFLVRDSSTSPGDYVLSVSENSRVSHYIINSSGPRPPVPPSPAQPPPGVSPSRLRIGDQEFDSLPALLEFYKIHYLDTTTLIEPVSRSRQGSGVILRQEEAEYVRALFDFNGNDEEDLPFKKGDILRIRDKPEEQWWNAEDSEGKRGMIPVPYVEKYRPASASVSALIGGN 204
               SCOP domains -----------d2eyya2 A:12-120 Crk proto-oncogen                                                                           -------------d2eyya1 A:134-190 C-Crk, N-terminal SH3 domain           -------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhhh........eee.......eeeee......eeeeee........................ee......hhhhhhhhh....................hhhhh.....eeee...................eeeeeeeee..eeeee.....eeee...................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------SH2  PDB: A:13-118 UniProt: 13-118                                                                        -------------SH3  PDB: A:132-192 UniProt: 132-192                         ------------ PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:1-81 UniProt: 1-81                                             --------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------Exon 1.2b  PDB: A:81-204 UniProt: 81-259 [INCOMPLETE]                                                                        Transcript 1 (2)
                 2eyy A   1 MAGNFDSEERSSWYWGRLSRQEAVALLQGQRHGVFLVRDSSTSPGDYVLSVSENSRVSHYIINSSGPRPPVPPSPAQPPPGVSPSRLRIGDQEFDSLPALLEFYKIHYLDTTTLIEPVSRSRQGSGVILRQEEAEYVRALFDFNGNDEEDLPFKKGDILRIRDKPEEQWWNAEDSEGKRGMIPVPYVEKYRPASASVSALIGGN 204
                                    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  (2, 2)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (CRK_HUMAN | P46108)
molecular function
    GO:0042169    SH2 domain binding    Interacting selectively and non-covalently with a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class.
    GO:0005070    SH3/SH2 adaptor activity    Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68).
    GO:0046875    ephrin receptor binding    Interacting selectively and non-covalently with an ephrin receptor.
    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:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0045309    protein phosphorylated amino acid binding    Interacting selectively and non-covalently with a phosphorylated amino acid residue within a protein.
biological process
    GO:0038096    Fc-gamma receptor signaling pathway involved in phagocytosis    An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
    GO:0000186    activation of MAPKK activity    The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK).
    GO:0048013    ephrin receptor signaling pathway    The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
    GO:0009967    positive regulation of signal transduction    Any process that activates or increases the frequency, rate or extent of signal transduction.
    GO:0043087    regulation of GTPase activity    Any process that modulates the rate of GTP hydrolysis by a GTPase.
    GO:0035020    regulation of Rac protein signal transduction    Any process that modulates the frequency, rate or extent of Rac protein signal transduction.
    GO:0032956    regulation of actin cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0048010    vascular endothelial growth factor receptor signaling pathway    Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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.

 Visualization

(-) 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)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(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 2eyy)
 
  Sites
(no "Sites" information available for 2eyy)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2eyy)
 

(-) Still Images

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

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2eyy
    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
  CRK_HUMAN | P46108
    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
  CRK_HUMAN | P46108
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CRK_HUMAN | P461081ju5 2dvj 2eyv 2eyw 2eyx 2eyz 2ms4

(-) Related Entries Specified in the PDB File

2eyv 2eyw 2eyx 2eyz