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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINAL FRAGMENT OF CBL-B
 
Authors :  Y. Kobashigawa, N. N. Noda, F. Inagaki
Date :  18 Aug 11  (Deposition) - 14 Dec 11  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Merohedral Twinning, E3 Ligase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kobashigawa, A. Tomitaka, H. Kumeta, N. N. Noda, M. Yamaguchi, F. Inagaki
Autoinhibition And Phosphorylation-Induced Activation Mechanisms Of Human Cancer And Autoimmune Disease-Related E Protein Cbl-B
Proc. Natl. Acad. Sci. Usa V. 108 20579 2011
PubMed-ID: 22158902  |  Reference-DOI: 10.1073/PNAS.1110712108

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE CBL-B
    Chains: A, B, C
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGBHPS
    Expression System Strain: ROSSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL FRAGMENT, UNP RESIDUES 39-426
    Gene: CBLB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3VGO)

(-) Sites  (0, 0)

(no "Site" information available for 3VGO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Pro A:71 -Pro A:72
2Gln A:241 -Pro A:242
3Pro B:71 -Pro B:72
4Gln B:241 -Pro B:242
5Pro C:71 -Pro C:72
6Gln C:241 -Pro C:242

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (8, 23)

Asymmetric Unit (8, 23)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2dENST000002641222dENSE00001340691chr3:105587887-105587580308CBLB_HUMAN-00--
1.3ENST000002641223ENSE00002109512chr3:105586435-105586254182CBLB_HUMAN1-56563A:43-56
B:43-56
C:43-56		14
14
14
1.4ENST000002641224ENSE00002192869chr3:105572508-105572258251CBLB_HUMAN57-140843A:57-140 (gaps)
B:57-140 (gaps)
C:57-140 (gaps)		84
84
84
1.5ENST000002641225ENSE00001686511chr3:105495386-105495240147CBLB_HUMAN140-189503A:140-189
B:140-189
C:140-189		50
50
50
1.6ENST000002641226ENSE00001628201chr3:105470462-105470306157CBLB_HUMAN189-241533A:189-241
B:189-241
C:189-241		53
53
53
1.7ENST000002641227ENSE00001692048chr3:105464882-105464761122CBLB_HUMAN242-282413A:242-282
B:242-282
C:242-282		41
41
41
1.8ENST000002641228ENSE00001696958chr3:105459475-105459338138CBLB_HUMAN282-328473A:282-328
B:282-328 (gaps)
C:282-328 (gaps)		47
47
47
1.9ENST000002641229ENSE00001616258chr3:105456102-10545601588CBLB_HUMAN328-357303A:328-339
B:328-339
C:328-338		12
12
11
1.10ENST0000026412210ENSE00001694160chr3:105452984-105452853132CBLB_HUMAN358-401442-
B:358-365
C:358-365		-
8
8
1.11ENST0000026412211ENSE00001654827chr3:105439094-105438891204CBLB_HUMAN402-469680--
1.12ENST0000026412212ENSE00001767402chr3:105423017-105422832186CBLB_HUMAN470-531620--
1.13aENST0000026412213aENSE00001607504chr3:105421303-105420938366CBLB_HUMAN532-6531220--
1.14ENST0000026412214ENSE00000774846chr3:105412432-10541233895CBLB_HUMAN654-685320--
1.15ENST0000026412215ENSE00000774845chr3:105404310-105404164147CBLB_HUMAN685-734500--
1.16bENST0000026412216bENSE00000774844chr3:105400662-10540056895CBLB_HUMAN734-766330--
1.16dENST0000026412216dENSE00000774843chr3:105400454-105400323132CBLB_HUMAN766-810450--
1.17ENST0000026412217ENSE00000774842chr3:105397415-105397275141CBLB_HUMAN810-857480--
1.18bENST0000026412218bENSE00000774841chr3:105389196-105389077120CBLB_HUMAN857-897410--
1.19dENST0000026412219dENSE00001755904chr3:105378073-1053743053769CBLB_HUMAN897-982860--

(-) 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:287
 aligned with CBLB_HUMAN | Q13191 from UniProtKB/Swiss-Prot  Length:982

    Alignment length:297
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       
           CBLB_HUMAN    43 RRTVEKTWKLMDKVVRLCQNPKLQLKNSPPYILDILPDTYQHLRLILSKYDDNQKLAQLSENEYFKIYIDSLMKKSKRAIRLFKEGKERMYEEQSQDRRNLTKLSLIFSHMLAEIKAIFPNGQFQGDNFRITKADAAEFWRKFFGDKTIVPWKVFRQCLHEVHQISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWGSILRNWNFLAVTHPGYMAFLTYDEVKARLQKYSTKPGSYIFRLSCTRLGQWAIGYVTGDGNILQTIPHNKPLFQALIDGSREGFYLYPDGRSYNP 339
               SCOP domains d3vgoa1 A:43-169 automated matches                                                                                             d3vgoa2 A:170-255 automated matches                                                   d3vgoa3 A:256-339 automated matches                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh------.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhh...hhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhh.hhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhh.....eeeee.hhhh..eeeeee.....eeee.....hhhhhhhhhh......hhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3      Exon 1.4  PDB: A:57-140 (gaps) UniProt: 57-140                                      ------------------------------------------------Exon 1.6  PDB: A:189-241 UniProt: 189-241            Exon 1.7  PDB: A:242-282 UniProt: 242-282---------------------------------------------Exon 1.9     Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------Exon 1.5  PDB: A:140-189 UniProt: 140-189         --------------------------------------------------------------------------------------------Exon 1.8  PDB: A:282-328 UniProt: 282-328      ----------- Transcript 1 (2)
                 3vgo A  43 RRTVEKTWKLMDKVVRLCQNPKLQLKNSPPYILDILPDTYQHLRLILSKY------AQLSENEYFKIYIDSLMKKSKRAIRLFKEGKERMY----QDRRNLTKLSLIFSHMLAEIKAIFPNGQFQGDNFRITKADAAEFWRKFFGDKTIVPWKVFRQCLHEVHQISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWGSILRNWNFLAVTHPGYMAFLTYDEVKARLQKYSTKPGSYIFRLSCTRLGQWAIGYVTGDGNILQTIPHNKPLFQALIDGSREGFYLYPDGRSYNP 339
                                    52        62        72        82        92      |102       112       122       132|    | 142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       
                                                                            92     99                               133  138                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:294
 aligned with CBLB_HUMAN | Q13191 from UniProtKB/Swiss-Prot  Length:982

    Alignment length:323
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362   
           CBLB_HUMAN    43 RRTVEKTWKLMDKVVRLCQNPKLQLKNSPPYILDILPDTYQHLRLILSKYDDNQKLAQLSENEYFKIYIDSLMKKSKRAIRLFKEGKERMYEEQSQDRRNLTKLSLIFSHMLAEIKAIFPNGQFQGDNFRITKADAAEFWRKFFGDKTIVPWKVFRQCLHEVHQISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWGSILRNWNFLAVTHPGYMAFLTYDEVKARLQKYSTKPGSYIFRLSCTRLGQWAIGYVTGDGNILQTIPHNKPLFQALIDGSREGFYLYPDGRSYNPDLTGLCEPTPHDHIKVTQEQYELYCE 365
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh-----.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----.hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhhh...eeehhhhhhhhhhhh...hhhhhhhhhhhhh.....eeehhhhhhhhhhh....hhhhhhhhhh.....eeee.hhhhhhhhhhhhh....eeeeee.......eeeeee.....eeee..--.hhhhhhhhhhhh....ee.......------------------.hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3      Exon 1.4  PDB: B:57-140 (gaps) UniProt: 57-140                                      ------------------------------------------------Exon 1.6  PDB: B:189-241 UniProt: 189-241            Exon 1.7  PDB: B:242-282 UniProt: 242-282---------------------------------------------Exon 1.9  PDB: B:328-339      1.10     Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------Exon 1.5  PDB: B:140-189 UniProt: 140-189         --------------------------------------------------------------------------------------------Exon 1.8  PDB: B:282-328 (gaps)                ------------------------------------- Transcript 1 (2)
                 3vgo B  43 RRTVEKTWKLMDKVVRLCQNPKLQLKNSPPYILDILPDTYQHLRLILSKYD-----AQLSENEYFKIYIDSLMKKSKRAIRLFKEGKERMY----QDRRNLTKLSLIFSHMLAEIKAIFPNGQFQGDNFRITKADAAEFWRKFFGDKTIVPWKVFRQCLHEVHQISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWGSILRNWNFLAVTHPGYMAFLTYDEVKARLQKYSTKPGSYIFRLSCTRLGQWAIGYVTGDGNILQTIP--KPLFQALIDGSREGFYLYPDGRSYNP------------------EQYELYCE 365
                                    52        62        72        82        92|     |102       112       122       132|    | 142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302        |- |     322       332      |  -         -     | 362   
                                                                             93    99                               133  138                                                                                                                                                                          311  |                      339                358       
                                                                                                                                                                                                                                                                                                         314                                                   


Chain C from PDB  Type:PROTEIN  Length:292
 aligned with CBLB_HUMAN | Q13191 from UniProtKB/Swiss-Prot  Length:982

    Alignment length:323
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362   
           CBLB_HUMAN    43 RRTVEKTWKLMDKVVRLCQNPKLQLKNSPPYILDILPDTYQHLRLILSKYDDNQKLAQLSENEYFKIYIDSLMKKSKRAIRLFKEGKERMYEEQSQDRRNLTKLSLIFSHMLAEIKAIFPNGQFQGDNFRITKADAAEFWRKFFGDKTIVPWKVFRQCLHEVHQISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWGSILRNWNFLAVTHPGYMAFLTYDEVKARLQKYSTKPGSYIFRLSCTRLGQWAIGYVTGDGNILQTIPHNKPLFQALIDGSREGFYLYPDGRSYNPDLTGLCEPTPHDHIKVTQEQYELYCE 365
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----.hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhh....eeehhhhhhhhhhhh...hhhhhhhhhhhhh.....eeehhhhhhhhhhh....hhhhhhhhhh.....eeee.hhhhhhhhhhhhh.....eeeee.......eeeeee.....eeee..--.hhhhhhhhhhhh....hhhhh...-------------------.hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3      Exon 1.4  PDB: C:57-140 (gaps) UniProt: 57-140                                      ------------------------------------------------Exon 1.6  PDB: C:189-241 UniProt: 189-241            Exon 1.7  PDB: C:242-282 UniProt: 242-282---------------------------------------------Exon 1.9  PDB: C:328-338      1.10     Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------Exon 1.5  PDB: C:140-189 UniProt: 140-189         --------------------------------------------------------------------------------------------Exon 1.8  PDB: C:282-328 (gaps)                ------------------------------------- Transcript 1 (2)
                 3vgo C  43 RRTVEKTWKLMDKVVRLCQNPKLQLKNSPPYILDILPDTYQHLRLILSKY------AQLSENEYFKIYIDSLMKKSKRAIRLFKEGKERMY----QDRRNLTKLSLIFSHMLAEIKAIFPNGQFQGDNFRITKADAAEFWRKFFGDKTIVPWKVFRQCLHEVHQISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWGSILRNWNFLAVTHPGYMAFLTYDEVKARLQKYSTKPGSYIFRLSCTRLGQWAIGYVTGDGNILQTIP--KPLFQALIDGSREGFYLYPDGRSYN-------------------EQYELYCE 365
                                    52        62        72        82        92      |102       112       122       132|    | 142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302        |- |     322       332     |   -         -     | 362   
                                                                            92     99                               133  138                                                                                                                                                                          311  |                     338                 358       
                                                                                                                                                                                                                                                                                                         314
   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
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (CBLB_HUMAN | Q13191)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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: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:0006607    NLS-bearing protein import into nucleus    The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.
    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:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0023051    regulation of signaling    Any process that modulates the frequency, rate or extent of a signaling process.
    GO:0009629    response to gravity    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gravitational stimulus.
    GO:0009725    response to hormone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
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:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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  3vgo
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  CBLB_HUMAN | Q13191
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 Related Entries

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

UniProtKB/Swiss-Prot
        CBLB_HUMAN | Q13191: 2ak5 2bz8 2do6 2j6f 2jnh 2ldr 2ooa 2oob 3pfv 3zni

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3VGO)