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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TYROSINE KINASE BINDING DOMAIN OF CBL-C (PL MUTANT)
 
Authors :  K. Takeshita, T. Tezuka, Y. Isozaki, E. Yamashita, M. Suzuki, Y. Yamana T. Yamamoto, A. Nakagawa
Date :  13 Apr 12  (Deposition) - 06 Mar 13  (Release) - 06 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Ptb Domain, Tkb (Tyrosine Kinase Binding) Domain, Four-Helix Bundle (4H), Calcium-Binding Ef Hand, Divergent Sh2 Domain, Regulator Of Egfr Mediated Signal Transduction, Ubiquitously Expressed, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Takeshita, T. Tezuka, Y. Isozaki, E. Yamashita, M. Suzuki, M. Kim, Y. Yamanashi, T. Yamamoto, A. Nakagawa
Structural Flexibility Regulates Phosphopeptide-Binding Activity Of The Tyrosine Kinase Binding Domain Of Cbl-C.
J. Biochem. V. 152 487 2012
PubMed-ID: 22888118  |  Reference-DOI: 10.1093/JB/MVS085

(-) Compounds

Molecule 1 - SIGNAL TRANSDUCTION PROTEIN CBL-C
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX6P-1
    Expression System StrainDH5A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentTYROSINE KINASE BINDING DOMAIN
    GeneCBLC
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRING FINGER PROTEIN 57, SH3-BINDING PROTEIN CBL-3, SH3- BINDING PROTEIN CBL-C

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:199 , THR A:201 , SER A:203 , HIS A:205 , GLU A:210BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWAREASP B:199 , THR B:201 , SER B:203 , HIS B:205 , GLU B:210 , HOH B:507BINDING SITE FOR RESIDUE CA B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:41 -Pro A:42
2Gln A:219 -Pro A:220
3Pro B:41 -Pro B:42
4Gln B:219 -Pro B:220

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VRQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3VRQ)

(-) Sequences/Alignments

Asymmetric 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:278
 aligned with CBLC_HUMAN | Q9ULV8 from UniProtKB/Swiss-Prot  Length:474

    Alignment length:310
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320
           CBLC_HUMAN    11 QWEEARALGRAVRMLQRLEEQCVDPRLSVSPPSLRDLLPRTAQLLREVAHSRRAAGGGGPGGPGGSGDFLLIYLANLEAKSRQVAALLPPRGRRSANDELFRAGSRLRRQLAKLAIIFSHMHAELHALFPGGKYCGHMYQLTKAPAHTFWRESCGARCVLPWAEFESLLGTCHPVEPGCTALALRTTIDLTCSGHVSIFEFDVFTRLFQPWPTLLKNWQLLAVNHPGYMAFLTYDEVQERLQACRDKPGSYIFRPSCTRLGQWAIGYVSSDGSILQTIPANKPLSQVLLEGQKDGFYLYPDGKTHNPDLT 320
               SCOP domains -----------------------------------------------------------------------------------------------------------------------------------------d3vrqa1 A:148-233 automated matches                                                   d3vrqa2 A:234-320 automated matches                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.--------..hhhhhhhhhhhhhhhhhhhh-------.....hhhhhhhhhhhhhhhhhhhhhh.-----------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh...eeehhhhhhhhhh......hhhhhhhhhhhh.....eeehhhhhhhhhhh.hhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhh....eeeeee.......eeeeee.....eeee.....hhhhhhhhhhhh....ee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vrq A  11 QWEEARALGRAVRMLQRLEEQC--------PPSLRDLLPRTAQLLREVAHSR-------PGGPGGSGDFLLIYLANLEAKSRQVAAL-----------------SRLRRQLAKLAIIFSHMHAELHALFPGGKYCGHMYQLTKAPAHTFWRESCGARCVLPWAEFESLLGTCHPVEPGCTALALRTTIDLTCSGHVSIFEFDVFTRLFQPWPTLLKNWQLLAVNHPGYMAFLTYDEVQERLQACRDKPGSYIFRLSCTRLGQWAIGYVSSDGSILQTIPANKPLSQVLLEGQKDGFYLYPDGKTHNPDLT 320
                                    20        30 |       -|       50        60 |      70        80        90      |  -         -    |  120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320
                                                32       41                   62      70                         97               115                                                                                                                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:275
 aligned with CBLC_HUMAN | Q9ULV8 from UniProtKB/Swiss-Prot  Length:474

    Alignment length:309
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311         
           CBLC_HUMAN    12 WEEARALGRAVRMLQRLEEQCVDPRLSVSPPSLRDLLPRTAQLLREVAHSRRAAGGGGPGGPGGSGDFLLIYLANLEAKSRQVAALLPPRGRRSANDELFRAGSRLRRQLAKLAIIFSHMHAELHALFPGGKYCGHMYQLTKAPAHTFWRESCGARCVLPWAEFESLLGTCHPVEPGCTALALRTTIDLTCSGHVSIFEFDVFTRLFQPWPTLLKNWQLLAVNHPGYMAFLTYDEVQERLQACRDKPGSYIFRPSCTRLGQWAIGYVSSDGSILQTIPANKPLSQVLLEGQKDGFYLYPDGKTHNPDLT 320
               SCOP domains ----------------------      -------------------------     ----------------------------                  --------------------------------d3vrqb1 B:148-233 automated matches                                                   d3vrqb2 B:234-320 automated matches                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..------...hhhhhhhhhhhhhhhhhhhh..-----.....hhhhhhhhhhhhhhhhhhhhhh.------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh...eeehhhhhhhhhh...-----.hhhhhhhhh.....eeehhhhhhhhhhh.hhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhh....eeeeee.......eeeeee.....eeee.....hhhhhhhhhhhh....ee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vrq B  12 WEEARALGRAVRMLQRLEEQCV------SPPSLRDLLPRTAQLLREVAHSRRA-----PGGPGGSGDFLLIYLANLEAKSRQVAAL------------------RLRRQLAKLAIIFSHMHAELHALFPGGKYCGHMYQLTKAPAHTFWRESCGARCVLPWAEFESLLGTCHP-----TALALRTTIDLTCSGHVSIFEFDVFTRLFQPWPTLLKNWQLLAVNHPGYMAFLTYDEVQERLQACRDKPGSYIFRLSCTRLGQWAIGYVSSDGSILQTIPANKPLSQVLLEGQKDGFYLYPDGKTHNPDLT 320
                                    21        31 |      41        51        61  |     71        81        91     |   -         -    |  121       131       141       151       161       171       181  |    191       201       211       221       231       241       251       261       271       281       291       301       311         
                                                33     40                      64    70                         97                116                                                                 184   190                                                                                                                                  

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CBLC_HUMAN | Q9ULV8)
molecular function
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0005154    epidermal growth factor receptor binding    Interacting selectively and non-covalently with the epidermal growth factor receptor.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0001784    phosphotyrosine residue binding    Interacting selectively and non-covalently with a phosphorylated tyrosine residue within a protein.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    GO:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0043407    negative regulation of MAP kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of MAP kinase activity.
    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:0007175    negative regulation of epidermal growth factor-activated receptor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of EGF-activated receptor activity.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0042787    protein ubiquitination involved in ubiquitin-dependent protein catabolic process    The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
    GO:0023051    regulation of signaling    Any process that modulates the frequency, rate or extent of a signaling process.
cellular component
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CBLC_HUMAN | Q9ULV83op0 3vrn 3vro 3vrp 3vrr

(-) Related Entries Specified in the PDB File

3vrn 3vro 3vrp 3vrr