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(-) Description

Title :  C-TERMINAL DOMAIN OF INSULIN-LIKE GROWTH FACTOR (IGF) BINDING PROTEIN-6: STRUCTURE AND INTERACTION WITH IGF-II
 
Authors :  S. J. Headey, D. W. Keizer, S. Yao, G. Brasier, P. Kantharidis, L. A. Bach, R. S. Norton
Date :  28 Nov 03  (Deposition) - 14 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Insulin-Like Growth Factor Binding Protein, Hormone/Growth Factor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. J. Headey, D. W. Keizer, S. Yao, G. Brasier, P. Kantharidis, L. A. Bach, R. S. Norton
C-Terminal Domain Of Insulin-Like Growth Factor (Igf) Binding Protein-6: Structure And Interaction With Igf-Ii.
Mol. Endocrinol. V. 18 2740 2004
PubMed-ID: 15308688  |  Reference-DOI: 10.1210/ME.2004-0248
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN 6
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPPROEX HTB
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DOMAIN, SEQUENCE DATABASE RESIUDE 161- 240
    GeneIGFBP6, IBP6
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIGFBP-6, IBP-6, IGF-BINDING PROTEIN 6

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1RMJ)

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:3 -A:30
2A:41 -A:52
3A:54 -A:74

(-) 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, 20Gly A:50 -Pro A:51

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

NMR Structure (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018933R217QIBP6_HUMANPolymorphism6413498AR57Q
2UniProtVAR_011907T236PIBP6_HUMANPolymorphism1053134AT76P

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYROGLOBULIN_1_2PS51162 Thyroglobulin type-1 domain profile.IBP6_HUMAN160-234  1A:1-74
2THYROGLOBULIN_1_1PS00484 Thyroglobulin type-1 repeat signature.IBP6_HUMAN186-219  1A:26-59

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003014641ENSE00001116916chr12:53491436-53491835400IBP6_HUMAN1-1121121A:-27--3 (gaps)41
1.2ENST000003014642ENSE00001116922chr12:53494496-53494641146IBP6_HUMAN112-160491A:-3--13
1.3ENST000003014643ENSE00001116923chr12:53494825-53494944120IBP6_HUMAN161-200401A:1-4040
1.4ENST000003014644ENSE00001116919chr12:53495829-53496128300IBP6_HUMAN201-240401A:41-8040

(-) 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:107
 aligned with IBP6_HUMAN | P24592 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:169
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231         
           IBP6_HUMAN    72 GVYTPNCAPGLQCHPPKDDEAPLRALLLGRGRCLPARAPAVAEENPKESKPQAGTARPQDVNRRDQQRNPGTSTTPSQPNSAGVQDTEMGPCRRHLDSVLQQLQTEVYRGAQTLYVPNCDHRGFYRKRQCRSSQGQRRGPCWCVDRMGKSLPGSPDGNGSSSCPTGSSG 240
               SCOP domains d1r        mja_ A: Insulin-like         gro                                              wth factor binding protein 6                                                     SCOP domains
               CATH domains ----------------------1rmjA01 A        :-13                                              -62 Invariant Chain; Chain I                                  ------------------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------Thyroglobulin_1-1rmjA01 A:3-74                                          ------ Pfam domains
         Sec.struct. author ...--------...........hhhhhh...--------....----------------------------------------------hhhhhhhhhhhhhhhhhh.....eeeee..........eeeeee.......eee.......................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------Q------------------P---- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------THYROGLOBULIN_1_2  PDB: A:1-74 UniProt: 160-234                            ------ PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------THYROGLOBULIN_1_1  PDB: A:26-59   --------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: A:-27--3 (gaps)           ------------------------------------------------Exon 1.3  PDB: A:1-40 UniProt: 161-200  Exon 1.4  PDB: A:41-80 UniProt: 201-240  Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.2  PDB: A:-3--1 UniProt: 112-160          -------------------------------------------------------------------------------- Transcript 1 (2)
                 1rmj A -27 SYY--------HHHHHHDYDIPTTENLYFQG--------AMGS----------------------------------------------GPCRRHLDSVLQQLQTEVYRGAQTLYVPNCDHRGFYRKRQCRSSQGQRRGPCWCVDRMGKSLPGSPDGNGSSSCPTGSSG  80
                              |      - |     -16        -6|       -4  |      -         -         -         -         1        11        21        31        41        51        61        71         
                              |      -24                 -5       -4 -1                                              1                                                                               
                            -25                                                                                                                                                                      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)
Chain A   (IBP6_HUMAN | P24592)
molecular function
    GO:0019838    growth factor binding    Interacting selectively and non-covalently with any growth factor, proteins or polypeptides that stimulate a cell or organism to grow or proliferate.
    GO:0031994    insulin-like growth factor I binding    Interacting selectively and non-covalently with insulin-like growth factor I.
    GO:0031995    insulin-like growth factor II binding    Interacting selectively and non-covalently with insulin-like growth factor II.
    GO:0005520    insulin-like growth factor binding    Interacting selectively and non-covalently with an insulin-like growth factor, any member of a group of polypeptides that are structurally homologous to insulin and share many of its biological activities, but are immunologically distinct from it.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0090090    negative regulation of canonical Wnt signaling pathway    Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0001558    regulation of cell growth    Any process that modulates the frequency, rate, extent or direction of cell growth.
    GO:0043567    regulation of insulin-like growth factor receptor signaling pathway    Any process that modulates the frequency, rate or extent of insulin-like growth factor receptor signaling.
    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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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    Gly A:50 - Pro A:51   [ RasMol ]  
 

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