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(-) Description

Title :  CRYSTAL STRUCTURE OF C-CBL-TKB DOMAIN COMPLEXED WITH ITS BINDING MOTIF IN SPROUTY4
 
Authors :  C. Ng, R. A. Jackson, J. P. Buschdorf, Q. Sun, G. R. Guy, J. Sivaraman
Date :  03 Jan 08  (Deposition) - 26 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Cbl, Tkb, Ligase, Signal Transduction, Proto-Oncogene, Complex, Alternative Splicing, Cytoplasm, Developmental Protein, Membrane, Calcium, Metal-Binding, Phosphoprotein, Sh2 Domain, Ubl Conjugation Pathway, Zinc, Zinc-Finger, Ligase/Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Ng, R. A. Jackson, J. P. Buschdorf, Q. Sun, G. R. Guy, J. Sivaraman
Structural Basis For A Novel Intrapeptidyl H-Bond And Reverse Binding Of C-Cbl-Tkb Domain Substrates
Embo J. V. 27 804 2008
PubMed-ID: 18273061  |  Reference-DOI: 10.1038/EMBOJ.2008.18
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 13-MERIC PEPTIDE FROM PORTEIN SPROUTY HOMOLOG 4
    ChainsA
    EngineeredYES
    FragmentUNP RESIDUES 46-58, PTYR-53 PHOSPHOPEPTIDE
    Other DetailsSYNTHETIC CONSTRUCT
    SynonymSPRY-4, SPROUTY-4
    SyntheticYES
 
Molecule 2 - E3 UBIQUITIN-PROTEIN LIGASE CBL
    ChainsB
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX4T1
    Expression System StrainROSETTA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentC-CBL TKB DOMAIN, CBL N-TERMINAL, UNP RESIDUES 23-351
    GeneCBL, CBL2, RNF55
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSIGNAL TRANSDUCTION PROTEIN CBL, PROTO-ONCOGENE C- CBL, CASITAS B-LINEAGE LYMPHOMA PROTO-ONCOGENE, RING FINGER PROTEIN 55

 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, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1PTR-1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (0, 0)

(no "Site" information available for 3BUN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro B:81 -Pro B:82
2Gln B:249 -Pro B:250

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_071040K287RCBL_HUMANUnclassified  ---BK287R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (0, 0)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_071040K287RCBL_HUMANUnclassified  ---BK287R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_071040K287RCBL_HUMANUnclassified  ---BK287R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (7, 7)

Asymmetric Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002640331ENSE00001240819chr11:119076752-119077322571CBL_HUMAN1-65651B:48-6518
1.2ENST000002640332ENSE00001240799chr11:119103158-119103405248CBL_HUMAN66-148831B:66-14883
1.3ENST000002640333ENSE00001240795chr11:119142445-119142591147CBL_HUMAN148-197501B:148-19750
1.4ENST000002640334ENSE00001240790chr11:119144578-119144734157CBL_HUMAN197-249531B:197-24953
1.5ENST000002640335ENSE00001240782chr11:119145542-119145663122CBL_HUMAN250-290411B:250-29041
1.6ENST000002640336ENSE00001240776chr11:119146707-119146844138CBL_HUMAN290-336471B:290-33647
1.7ENST000002640337ENSE00001128289chr11:119148467-11914855488CBL_HUMAN336-365301B:336-35116
1.8ENST000002640338ENSE00001795866chr11:119148876-119149007132CBL_HUMAN366-409440--
1.9ENST000002640339ENSE00001128273chr11:119149220-119149423204CBL_HUMAN410-477680--
1.10ENST0000026403310ENSE00000796209chr11:119155679-119155810132CBL_HUMAN478-521440--
1.11ENST0000026403311ENSE00001206751chr11:119155899-119156276378CBL_HUMAN522-6471260--
1.12ENST0000026403312ENSE00000796211chr11:119158562-11915865695CBL_HUMAN648-679320--
1.13ENST0000026403313ENSE00000796212chr11:119167628-119167744117CBL_HUMAN679-718400--
1.14ENST0000026403314ENSE00000796213chr11:119168094-11916819198CBL_HUMAN718-751340--
1.15ENST0000026403315ENSE00000796214chr11:119169068-119169250183CBL_HUMAN751-812620--
1.16ENST0000026403316ENSE00001238481chr11:119170205-1191776517447CBL_HUMAN812-906950--

(-) 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:7
 aligned with SPY4_HUMAN | Q9C004 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:7
           SPY4_HUMAN    50 NDYIDNP  56
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 3bun A  51 NDyIDNP  57
                              |    
                             53-PTR

Chain B from PDB  Type:PROTEIN  Length:304
 aligned with CBL_HUMAN | P22681 from UniProtKB/Swiss-Prot  Length:906

    Alignment length:304
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347    
            CBL_HUMAN    48 PGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPPYILDLLPDTYQHLRTILSRYEGKMETLGENEYFRVFMENLMKKTKQTISLFKEGKERMYEENSQPRRNLTKLSLIFSHMLAELKGIFPSGLFQGDTFRITKADAAEFWRKAFGEKTIVPWKSFRQALHEVHPISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWSSLLRNWNSLAVTHPGYMAFLTYDEVKARLQKFIHKPGSYIFRLSCTRLGQWAIGYVTADGNILQTIPHNKPLFQALIDGFREGFYLFPDGRNQNPDLTG 351
               SCOP domains d3bunb2 B:48-177 N-terminal domain of cbl (N-cbl)                                                                                 d3bunb1 B:178-263 Cbl                                                                 d3bunb3 B:264-351 Cbl                                                                    SCOP domains
               CATH domains 3bunB01 B:48-175  [code=1.20.930.20, no name defined]                                                                           3bunB02 B:176-264 EF-hand                                                                3bunB03 B:265-350 SHC Adaptor Protein                                                 - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhhh...eeehhhhhhhhhhhh...hhhhhhhhhhhhh.....eeehhhhhhhhhhh.hhhhhhhhhhhhh..........hhhhhhhhhhh......eeeeee.......eeeeee.....eeee.....hhhhhhhhhhhh....ee........... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1          Exon 1.2  PDB: B:66-148 UniProt: 66-148                                            ------------------------------------------------Exon 1.4  PDB: B:197-249 UniProt: 197-249            Exon 1.5  PDB: B:250-290 UniProt: 250-290---------------------------------------------Exon 1.7         Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------Exon 1.3  PDB: B:148-197 UniProt: 148-197         --------------------------------------------------------------------------------------------Exon 1.6  PDB: B:290-336 UniProt: 290-336      --------------- Transcript 1 (2)
                 3bun B  48 PGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPPYILDLLPDTYQHLRTILSRYEGKMETLGENEYFRVFMENLMKKTKQTISLFKEGKERMYEENSQPRRNLTKLSLIFSHMLAELKGIFPSGLFQGDTFRITKADAAEFWRKAFGEKTIVPWKSFRQALHEVHPISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWSSLLRNWNSLAVTHPGYMAFLTYDEVKARLQKFIHKPGSYIFRLSCTRLGQWAIGYVTADGNILQTIPHNKPLFQALIDGFREGFYLFPDGRNQNPDLTG 351
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347    

   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  (3, 3)

Asymmetric Unit

(-) CATH Domains  (3, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (39, 43)

Asymmetric Unit(hide GO term definitions)
Chain A   (SPY4_HUMAN | Q9C004)
molecular function
    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).
biological process
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0070373    negative regulation of ERK1 and ERK2 cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0009966    regulation of signal transduction    Any process that modulates the frequency, rate or extent of signal transduction.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination 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: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:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.

Chain B   (CBL_HUMAN | P22681)
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:0046875    ephrin receptor binding    Interacting selectively and non-covalently with an ephrin 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: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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    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:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    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:0007173    epidermal growth factor receptor signaling pathway    A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0008543    fibroblast growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    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:0045742    positive regulation of epidermal growth factor receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
    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:0048260    positive regulation of receptor-mediated endocytosis    Any process that activates or increases the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
    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.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007179    transforming growth factor beta receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    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:0016600    flotillin complex    A protein complex that contains flotillin-1 and flotillin-2, and may contain associated proteins. Flotillins associate into membrane microdomains resembling caveolae.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CBL_HUMAN | P226811b47 1fbv 1yvh 2cbl 2juj 2k4d 2oo9 2y1m 2y1n 3bum 3buo 3buw 3bux 3ob1 3ob2 3plf 4a49 4a4b 4a4c 4gpl 5hkw 5hkx 5hky 5hkz 5hl0 5j3x

(-) Related Entries Specified in the PDB File

3bum C-CBL-TKB DOMAIN COMPLEXED WITH ITS BINDING MOTIF IN SPROUTY2
3buo C-CBL-TKB DOMAIN COMPLEXED WITH ITS BINDING MOTIF IN EGF RECEPTOR
3buw C-CBL-TKB DOMAIN COMPLEXED WITH ITS BINDING MOTIF IN SYK
3bux C-CBL-TKB DOMAIN COMPLEXED WITH ITS BINDING MOTIF IN C-MET