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(-) Description

Title :  NMR STRUCTURE OF THE N-TERMINAL HATH DOMAIN OF HUMAN HDGF
 
Authors :  S. -C. Sue, J. -Y. Chen, T. -H. Huang
Date :  16 Nov 03  (Deposition) - 16 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Hdgf, Hath Domain, Pwwp Domain, Heparin-Binding, Growth Factor, Hormone/Growth Factor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. -C. Sue, J. -Y. Chen, S. -C. Lee, W. -G. Wu, T. -H. Huang
Solution Structure And Heparin Interaction Of Human Hepatoma-Derived Growth Factor
J. Mol. Biol. V. 343 1365 2004
PubMed-ID: 15491618  |  Reference-DOI: 10.1016/J.JMB.2004.09.014
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEPATOMA-DERIVED GROWTH FACTOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET11D
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL 100 RESIDUES
    GeneHDGF
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTHE HATH DOMAIN OF HHDGF, HDGF, HIGH-MOBILITY GROUP PROTEIN 1-LIKE 2, HMG-1L2

 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 1RI0)

(-) Sites  (0, 0)

(no "Site" information available for 1RI0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RI0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RI0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RI0)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PWWPPS50812 PWWP domain profile.HDGF_HUMAN12-69  1A:12-69

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.5aENST000003573255aENSE00001425593chr1:156721536-156721135402HDGF_HUMAN1-29291A:1-2929
1.7aENST000003573257aENSE00001054761chr1:156715165-15671508977HDGF_HUMAN30-55261A:30-5526
1.7cENST000003573257cENSE00001167827chr1:156714938-156714800139HDGF_HUMAN55-101471A:55-10046
1.9aENST000003573259aENSE00000959262chr1:156714140-156713955186HDGF_HUMAN102-163620--
1.10dENST0000035732510dENSE00001267769chr1:156713670-156713444227HDGF_HUMAN164-239760--
1.10jENST0000035732510jENSE00001922574chr1:156713247-1567118991349HDGF_HUMAN239-24020--

(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:100
 aligned with HDGF_HUMAN | P51858 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:100
                                    10        20        30        40        50        60        70        80        90       100
           HDGF_HUMAN     1 MSRSNRQKEYKCGDLVFAKMKGYPHWPARIDEMPEAAVKSTANKYQVFFFGTHETAFLGPKDLFPYEESKEKFGKPNKRKGFSEGLWEIENNPTVKASGY 100
               SCOP domains d1ri0a_ A: Hepatoma-derived growth factor, HDGF                                                      SCOP domains
               CATH domains -------------1ri0A01 A:14-94  [code=2.30.30.160, no name defined]                             ------ CATH domains
               Pfam domains --------PWWP-1ri0A01 A:9-81                                                      ------------------- Pfam domains
         Sec.struct. author ..............eeeeee..eeeeeeeee.............eeeee....eeeee....ee.hhhhhhh.......hhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------PWWP  PDB: A:12-69 UniProt: 12-69                         ------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5a  PDB: A:1-29       Exon 1.7a  PDB: A:30-55   --------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.7c  PDB: A:55-100 UniProt: 55-101       Transcript 1 (2)
                 1ri0 A   1 MSRSNRQKEYKCGDLVFAKMKGYPHWPARIDEMPEAAVKSTANKYQVFFFGTHETAFLGPKDLFPYEESKEKFGKPNKRKGFSEGLWEIENNPTVKASGY 100
                                    10        20        30        40        50        60        70        80        90       100

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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
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Tudor (88)

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (HDGF_HUMAN | P51858)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0001106    RNA polymerase II transcription corepressor activity    Interacting selectively and non-covalently with an RNA polymerase II repressing transcription factor and also with the RNA polymerase II basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0001222    transcription corepressor binding    Interacting selectively and non-covalently with a transcription corepressor, any protein involved in negative regulation of transcription via protein-protein interactions with transcription factors and other proteins that negatively regulate transcription. Transcription corepressors do not bind DNA directly, but rather mediate protein-protein interactions between repressing transcription factors and the basal transcription machinery.
biological process
    GO:0036498    IRE1-mediated unfolded protein response    A series of molecular signals mediated by the endoplasmic reticulum stress sensor IRE1 (Inositol-requiring transmembrane kinase/endonuclease). Begins with activation of IRE1 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. One target of activated IRE1 is the transcription factor HAC1 in yeast, or XBP1 in mammals; IRE1 cleaves an intron of a mRNA coding for HAC1/XBP1 to generate an activated HAC1/XBP1 transcription factor, which controls the up regulation of UPR-related genes. At least in mammals, IRE1 can also signal through additional intracellular pathways including JNK and NF-kappaB.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.
    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:0017053    transcriptional repressor complex    A protein complex that possesses activity that prevents or downregulates transcription.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HDGF_HUMAN | P518582nlu

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