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(-) Description

Title :  E2-C-CBL RECOGNITION IS NECESSARY BUT NOT SUFFICIENT FOR UBIQUITINATION ACTIVITY
 
Authors :  A. Huang, R. N. De Jong, H. Wienk, S. G. Winkler, H. T. M. Timmers, R. Boelens
Date :  06 Jun 08  (Deposition) - 20 Jan 09  (Release) - 20 Jan 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Protein, Nmr, Ubiquitin, C-Cbl, Ubch5B, Ubch7, Calcium, Cytoplasm, Ligase, Metal-Binding, Phosphoprotein, Proto- Oncogene, Sh2 Domain, Ubl Conjugation Pathway, Zinc, Zinc- Finger (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Huang, R. N. De Jong, H. Wienk, G. S. Winkler, H. T. M. Timmers, R. Boelens
E2-C-Cbl Recognition Is Necessary But Not Sufficient For Ubiquitination Activity
J. Mol. Biol. V. 385 507 2009
PubMed-ID: 18996392  |  Reference-DOI: 10.1016/J.JMB.2008.10.044
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE CBL
    ChainsA
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3) ROSETTA 2
    Expression System Taxid562
    Expression System VectorPLICHISGST
    Expression System Vector TypeVECTOR
    FragmentRING DOMAIN, RESIDUES 358-437
    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

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:381 , ILE A:383 , CYS A:384 , ASN A:387 , ASP A:388BINDING SITE FOR RESIDUE ZN A 500
2AC2SOFTWAREILE A:393 , CYS A:396 , HIS A:398 , CYS A:421BINDING SITE FOR RESIDUE ZN A 600

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:401 -A:404

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Glu A:394 -Pro A:395

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

NMR Structure (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_064332Q367PCBL_HUMANDisease (NSLL)267606704AQ367P
2UniProtVAR_071042Y371HCBL_HUMANUnclassified267606706AY371H
3UniProtVAR_064333K382ECBL_HUMANDisease (NSLL)267606705AK382E
4UniProtVAR_064334D390YCBL_HUMANDisease (NSLL)267606707AD390Y
5UniProtVAR_064335R420QCBL_HUMANDisease (NSLL)267606708AR420Q

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_RING_2PS50089 Zinc finger RING-type profile.CBL_HUMAN381-420  1A:381-420
2ZF_RING_1PS00518 Zinc finger RING-type signature.CBL_HUMAN396-405  1A:396-405

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002640331ENSE00001240819chr11:119076752-119077322571CBL_HUMAN1-65650--
1.2ENST000002640332ENSE00001240799chr11:119103158-119103405248CBL_HUMAN66-148830--
1.3ENST000002640333ENSE00001240795chr11:119142445-119142591147CBL_HUMAN148-197500--
1.4ENST000002640334ENSE00001240790chr11:119144578-119144734157CBL_HUMAN197-249530--
1.5ENST000002640335ENSE00001240782chr11:119145542-119145663122CBL_HUMAN250-290410--
1.6ENST000002640336ENSE00001240776chr11:119146707-119146844138CBL_HUMAN290-336470--
1.7ENST000002640337ENSE00001128289chr11:119148467-11914855488CBL_HUMAN336-365301A:355-365 (gaps)15
1.8ENST000002640338ENSE00001795866chr11:119148876-119149007132CBL_HUMAN366-409441A:366-40944
1.9ENST000002640339ENSE00001128273chr11:119149220-119149423204CBL_HUMAN410-477681A:410-43728
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

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:83
 aligned with CBL_HUMAN | P22681 from UniProtKB/Swiss-Prot  Length:906

    Alignment length:87
                                   360       370       380       390       400       410       420       430       
            CBL_HUMAN   351 GLCEPTPQDHIKVTQEQYELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPIVVDPFDPR 437
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------zf-C3HC4-2k4dA01 A:381-419             ------------------ Pfam domains
         Sec.struct. author .----...................................eeeee..eeehhhhhhhhhh............eeeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------P---H----------E-------Y-----------------------------Q----------------- SAPs(SNPs)
                PROSITE (1) ------------------------------ZF_RING_2  PDB: A:381-420               ----------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------ZF_RING_1 -------------------------------- PROSITE (2)
               Transcript 1 Exon 1.7       Exon 1.8  PDB: A:366-409 UniProt: 366-409   Exon 1.9  PDB: A:410-437     Transcript 1
                 2k4d A 355 G----SLQDHIKVTQEQYELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPIVVDPFDPR 437
                            |    | 360       370       380       390       400       410       420       430       
                            |  356                                                                                 
                          355                                                                                      

   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 2K4D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2K4D)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: RING (39)

(-) Gene Ontology  (32, 32)

NMR Structure(hide GO term definitions)
Chain A   (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 2oo9 2y1m 2y1n 3bum 3bun 3buo 3buw 3bux 3ob1 3ob2 3plf 4a49 4a4b 4a4c 4gpl 5hkw 5hkx 5hky 5hkz 5hl0 5j3x

(-) Related Entries Specified in the PDB File

1fbv C-CBL UBCH7 CRYSTAL STRUCTURE RELATED ID: 15796 RELATED DB: BMRB