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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RA AND PH DOMAINS OF GRB10
 
Authors :  S. R. Hubbard, R. S. Depetris, J. Wu
Date :  22 May 09  (Deposition) - 04 Aug 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Grb10, Ra, Ph, Ras-Associating, Pleckstrin-Homology, Adapter Protein, Phosphoprotein, Sh2 Domain, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. S. Depetris, J. Wu, S. R. Hubbard
Structural And Functional Studies Of The Ras-Associating An Pleckstrin-Homology Domains Of Grb10 And Grb14.
Nat. Struct. Mol. Biol. V. 16 833 2009
PubMed-ID: 19648926  |  Reference-DOI: 10.1038/NSMB.1642

(-) Compounds

Molecule 1 - GROWTH FACTOR RECEPTOR-BOUND PROTEIN 10
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET14B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRAS-ASSOCIATING DOMAIN, PH DOMAIN, UNP RESIDUES 164-415
    GeneGRB10, GRBIR, KIAA0207
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGRB10 ADAPTER PROTEIN, INSULIN RECEPTOR-BINDING PROTEIN GRB- IR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SCN1Ligand/IonTHIOCYANATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:193 , PHE A:197 , THR A:334 , ARG A:337BINDING SITE FOR RESIDUE SCN A 15

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HK0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HK0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HK0)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.GRB10_HUMAN290-399
 
  2A:233-341
B:233-341

(-) Exons   (8, 16)

Asymmetric/Biological Unit (8, 16)
 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_HUMAN121-168482A:109-110
B:110-110
2
1
1.22aENST0000039881222aENSE00001727478chr7:50694675-50694519157GRB10_HUMAN169-221532A:111-163 (gaps)
B:111-163 (gaps)
53
53
1.23ENST0000039881223ENSE00001632392chr7:50686982-50686867116GRB10_HUMAN221-259392A:163-201
B:163-201
39
39
1.24aENST0000039881224aENSE00001626202chr7:50685836-5068576869GRB10_HUMAN260-282232A:202-224 (gaps)
B:202-224 (gaps)
23
23
1.25ENST0000039881225ENSE00001673533chr7:50684044-50683907138GRB10_HUMAN283-328462A:225-270
B:225-264
46
40
1.26ENST0000039881226ENSE00001798287chr7:50682577-50682467111GRB10_HUMAN329-365372A:271-307
B:275-307
37
33
1.27ENST0000039881227ENSE00001654867chr7:50680536-5068043899GRB10_HUMAN366-398332A:308-340
B:308-340
33
33
1.28bENST0000039881228bENSE00001668857chr7:50674111-5067403478GRB10_HUMAN399-424262A:341-351
B:341-350
11
10
1.29aENST0000039881229aENSE00001635907chr7:50673103-50672987117GRB10_HUMAN425-463390--
1.30ENST0000039881230ENSE00001789276chr7:50672074-5067200867GRB10_HUMAN464-486230--
1.31ENST0000039881231ENSE00001358450chr7:50671782-5067169588GRB10_HUMAN486-515300--
1.32cENST0000039881232cENSE00000683078chr7:50663227-5066313494GRB10_HUMAN515-546320--
1.33fENST0000039881233fENSE00001358289chr7:50660795-506577603036GRB10_HUMAN547-594480--

(-) 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:230
 aligned with GRB10_HUMAN | Q13322 from UniProtKB/Swiss-Prot  Length:594

    Alignment length:243
                                   176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406   
          GRB10_HUMAN   167 KQDVKVFSEDGTSKVVEILADMTARDLCQLLVYKSHCVDDNSWTLVEHHPHLGLERCLEDHELVVQVESTMASESKFLFRKNYAKYEFFKNPMNFFPEQMVTWCQQSNGSQTQLLQNFLNSSSCPEIQGFLHVKELGKKSWKKLYVCLRRSGLYCSTKGTSKEPRHLQLLADLEDSNIFSLIAGRKQYNAPTDHGLCIKPNKVRNETKELRLLCAEDEQTRTCWMTAFRLLKYGMLLYQNYRI 409
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eeeeee....hhhhhhhhhhh.-------.eeeeeee....eeee.....hhhhhhhh.....eeeeee....hhhhhhhhhh.....eee....------hhhhhhh....eeeeeeeeee......eeeeeeeee..eeeee......hhh.eeeee....eeeeee..hhhhhh....eeeeeee..........eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------PH_DOMAIN  PDB: A:233-341 UniProt: 290-399                                                                    ---------- PROSITE
           Transcript 1 (1) 1.Exon 1.22a  PDB: A:111-163 (gaps) UniProt: 169-221   --------------------------------------Exon 1.24a             Exon 1.25  PDB: A:225-270 UniProt: 283-328    Exon 1.26  PDB: A:271-307            Exon 1.27  PDB: A:308-340        Exon 1.28b  Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.23  PDB: A:163-201              ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3hk0 A 109 KQDVKVFSEDGTSKVVEILADMTARDLCQLLVYK-------SWTLVEHHPHLGLERCLEDHELVVQVESTMASESKFLFRKNYAKYEFFKNPMNFFPEQMVTWSQQS------LLQNFLNSSSSPEIQGFLHVKELGKKSWKKLYVCLRRSGLYCSTKGTSAAPRHLQLLADLEDSNIFSLIAGRKQYNAPTDHGLCIKPNKVRNETKELRLLCAEDEQTRTSWMTAFRLLKYGMLLYQNYRI 351
                                   118       128       138   |     - |     158       168       178       188       198       208      |  -   |   228       238       248       258       268       278       288       298       308       318       328       338       348   
                                                           142     150                                                              215    222                                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:216
 aligned with GRB10_HUMAN | Q13322 from UniProtKB/Swiss-Prot  Length:594

    Alignment length:241
                                   177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407 
          GRB10_HUMAN   168 QDVKVFSEDGTSKVVEILADMTARDLCQLLVYKSHCVDDNSWTLVEHHPHLGLERCLEDHELVVQVESTMASESKFLFRKNYAKYEFFKNPMNFFPEQMVTWCQQSNGSQTQLLQNFLNSSSCPEIQGFLHVKELGKKSWKKLYVCLRRSGLYCSTKGTSKEPRHLQLLADLEDSNIFSLIAGRKQYNAPTDHGLCIKPNKVRNETKELRLLCAEDEQTRTCWMTAFRLLKYGMLLYQNYR 408
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhh.------..eeeeeee....eeee.....hhhhhhhh.....eeeeee....hhhhhh.........ee..---------hhhhhhh.....eeeeeeeee......eeeeeeeee..eeee.----------.eeee....eeeeee.............eeeeee...........eee..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------PH_DOMAIN  PDB: B:233-341 UniProt: 290-399                                                                    --------- PROSITE
           Transcript 1 (1) 1Exon 1.22a  PDB: B:111-163 (gaps) UniProt: 169-221   --------------------------------------Exon 1.24a             Exon 1.25  PDB: B:225-264 UniProt: 283-328    Exon 1.26  PDB: B:275-307            Exon 1.27  PDB: B:308-340        Exon 1.28b Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.23  PDB: B:163-201              ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3hk0 B 110 QDVKVFSEDGTSKVVEILADMTARDLCQLLVYK------NSWTLVEHHPHLGLERCLEDHELVVQVESTMASESKFLFRKNYAKYEFFKNPMNFFPEQMVTWS---------LLQNFLNSSSSPEIQGFLHVKELGKKSWKKLYVCLRRSGLYCS----------LQLLADLEDSNIFSLIAGRKQYNAPTDHGLCIKPNKVRNETKELRLLCAEDEQTRTSWMTAFRLLKYGMLLYQNYR 350
                                   119       129       139  |    149       159       169       179       189       199       209  |      -  |    229       239       249       259    |    -     | 279       289       299       309       319       329       339       349 
                                                          142    149                                                            212       222                                       264        275                                                                           

   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 3HK0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HK0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HK0)

(-) 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 | Q133221nrv

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