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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SH2 DOMAIN OF GRB10
 
Authors :  E. G. Stein, S. R. Hubbard
Date :  25 Jan 03  (Deposition) - 15 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dimer, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. G. Stein, R. Ghirlando, S. R. Hubbard
Structural Basis For Dimerization Of The Grb10 Src Homology 2 Domain. Implications For Ligand Specificity.
J. Biol. Chem. V. 278 13257 2003
PubMed-ID: 12551896  |  Reference-DOI: 10.1074/JBC.M212026200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GROWTH FACTOR RECEPTOR-BOUND PROTEIN 10
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET21
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentSH2 DOMAIN
    GeneGRB10 OR GRBIR OR KIAA0207
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGRB10 ADAPTER PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1NRV)

(-) Sites  (0, 0)

(no "Site" information available for 1NRV)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NRV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NRV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_053113D558HGRB10_HUMANPolymorphism11768472A/BD500H

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.GRB10_HUMAN493-589
 
  2A:435-531
B:435-531

(-) Exons   (3, 6)

Asymmetric/Biological Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.12bENST0000039881212bENSE00002179678chr7:50800050-5079996982GRB10_HUMAN1-17170--
1.19ENST0000039881219ENSE00001720914chr7:50771605-5077151888GRB10_HUMAN18-47300--
1.20ENST0000039881220ENSE00002188279chr7:50742355-50742133223GRB10_HUMAN47-121750--
1.21ENST0000039881221ENSE00001695732chr7:50737560-50737419142GRB10_HUMAN121-168480--
1.22aENST0000039881222aENSE00001727478chr7:50694675-50694519157GRB10_HUMAN169-221530--
1.23ENST0000039881223ENSE00001632392chr7:50686982-50686867116GRB10_HUMAN221-259390--
1.24aENST0000039881224aENSE00001626202chr7:50685836-5068576869GRB10_HUMAN260-282230--
1.25ENST0000039881225ENSE00001673533chr7:50684044-50683907138GRB10_HUMAN283-328460--
1.26ENST0000039881226ENSE00001798287chr7:50682577-50682467111GRB10_HUMAN329-365370--
1.27ENST0000039881227ENSE00001654867chr7:50680536-5068043899GRB10_HUMAN366-398330--
1.28bENST0000039881228bENSE00001668857chr7:50674111-5067403478GRB10_HUMAN399-424260--
1.29aENST0000039881229aENSE00001635907chr7:50673103-50672987117GRB10_HUMAN425-463390--
1.30ENST0000039881230ENSE00001789276chr7:50672074-5067200867GRB10_HUMAN464-486230--
1.31ENST0000039881231ENSE00001358450chr7:50671782-5067169588GRB10_HUMAN486-515302A:429-457
B:429-457
29
29
1.32cENST0000039881232cENSE00000683078chr7:50663227-5066313494GRB10_HUMAN515-546322A:457-488
B:457-488
32
32
1.33fENST0000039881233fENSE00001358289chr7:50660795-506577603036GRB10_HUMAN547-594482A:489-533 (gaps)
B:489-533 (gaps)
45
45

(-) Sequences/Alignments

Asymmetric/Biological 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:100
 aligned with GRB10_HUMAN | Q13322 from UniProtKB/Swiss-Prot  Length:594

    Alignment length:105
                                   496       506       516       526       536       546       556       566       576       586     
          GRB10_HUMAN   487 IHRTQHWFHGRISREESHRIIKQQGLVDGLFLLRDSQSNPKAFVLTLCHHQKIKNFQILPCEDDGQTFFSLDDGNTKFSDLIQLVDFYQLNKGVLPCKLKHHCIR 591
               SCOP domains d1nrva_ A: Growth factor receptor-bound protein 10, GRB10                                                 SCOP domains
               CATH domains 1nrvA00 A:429-533 SHC Adaptor Protein                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhh.....eeeeee.......eeeeeee..eeeeeeeee.-----..ee.........hhhhhhhhhh...........ee... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------H--------------------------------- SAPs(SNPs)
                    PROSITE ------SH2  PDB: A:435-531 UniProt: 493-589                                                             -- PROSITE
           Transcript 1 (1) Exon 1.31  PDB: A:429-457    -------------------------------Exon 1.33f  PDB: A:489-533 (gaps)             Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.32c  PDB: A:457-488      --------------------------------------------- Transcript 1 (2)
                 1nrv A 429 IHRTQHWFHGRISREESHRIIKQQGLVDGLFLLRDSQSNPKAFVLTLCHHQKIKNFQILPC-----TFFSLDDGNTKFSDLIQLVDFYQLNKGVLPCKLKHHCIR 533
                                   438       448       458       468       478       488|     |498       508       518       528     
                                                                                      489   495                                      

Chain B from PDB  Type:PROTEIN  Length:100
 aligned with GRB10_HUMAN | Q13322 from UniProtKB/Swiss-Prot  Length:594

    Alignment length:105
                                   496       506       516       526       536       546       556       566       576       586     
          GRB10_HUMAN   487 IHRTQHWFHGRISREESHRIIKQQGLVDGLFLLRDSQSNPKAFVLTLCHHQKIKNFQILPCEDDGQTFFSLDDGNTKFSDLIQLVDFYQLNKGVLPCKLKHHCIR 591
               SCOP domains d1nrvb_ B: Growth factor receptor-bound protein 10, GRB10                                                 SCOP domains
               CATH domains 1nrvB00 B:429-533 SHC Adaptor Protein                                                                     CATH domains
           Pfam domains (1) ------SH2-1nrvB01 B:435-516                                                             ----------------- Pfam domains (1)
           Pfam domains (2) ------SH2-1nrvB02 B:435-516                                                             ----------------- Pfam domains (2)
         Sec.struct. author ............hhhhhhhhhhhh.....eeeeee.......eeeeeee..eeeeeeeee.-----..ee.........hhhhhhhhhh...........ee... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------H--------------------------------- SAPs(SNPs)
                    PROSITE ------SH2  PDB: B:435-531 UniProt: 493-589                                                             -- PROSITE
           Transcript 1 (1) Exon 1.31  PDB: B:429-457    -------------------------------Exon 1.33f  PDB: B:489-533 (gaps)             Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.32c  PDB: B:457-488      --------------------------------------------- Transcript 1 (2)
                 1nrv B 429 IHRTQHWFHGRISREESHRIIKQQGLVDGLFLLRDSQSNPKAFVLTLCHHQKIKNFQILPC-----TFFSLDDGNTKFSDLIQLVDFYQLNKGVLPCKLKHHCIR 533
                                   438       448       458       468       478       488|     |498       508       518       528     
                                                                                      489   495                                      

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Family: SH2 (119)
1aSH2-1nrvB01B:435-516
1bSH2-1nrvB02B:435-516

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GRB10_HUMAN | Q13322)
molecular function
    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:0005158    insulin receptor binding    Interacting selectively and non-covalently with the insulin 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).
biological process
    GO:0008286    insulin receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
    GO:0048009    insulin-like growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin-like growth factor receptor binding to one of its physiological ligands.
    GO:0030178    negative regulation of Wnt signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway.
    GO:0046325    negative regulation of glucose import    Any process that stops, prevents, or reduces the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle.
    GO:0045719    negative regulation of glycogen biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen.
    GO:0046627    negative regulation of insulin receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of insulin receptor signaling.
    GO:0042326    negative regulation of phosphorylation    Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
    GO:0042327    positive regulation of phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
    GO:0030949    positive regulation of vascular endothelial growth factor receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity.
    GO:0032868    response to insulin    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 an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    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: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
        GRB10_HUMAN | Q133223hk0

(-) Related Entries Specified in the PDB File

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