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(-) Description

Title :  THE NMR STRUCTURES OF A WINGED HELIX PROTEIN: GENESIS, 20 STRUCTURES
 
Authors :  I. Marsden, C. Jin, X. Liao
Date :  27 Jan 98  (Deposition) - 17 Jun 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Hnf-3 Homologues, Winged Helix Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. Marsden, C. Jin, X. Liao
Structural Changes In The Region Directly Adjacent To The Dna-Binding Helix Highlight A Possible Mechanism To Explain The Observed Changes In The Sequence-Specific Binding Of Winged Helix Proteins.
J. Mol. Biol. V. 278 293 1998
PubMed-ID: 9571051  |  Reference-DOI: 10.1006/JMBI.1998.1703
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GENESIS
    Cellular LocationNUCLEUS
    Cell Line293
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System GeneT7
    Expression System OrganelleINCLUSION BODIES
    Expression System PlasmidPET21
    Expression System StrainHMS-174
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentDNA-BINDING DOMAIN
    GeneHFH-2, GENESIS
    OrganLIVER, LUNG, HEART
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    Other DetailsFIRST PUBLISHED IN PNAS 90, 3948-3952
    SynonymHFH-2

 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 2HFH)

(-) Sites  (0, 0)

(no "Site" information available for 2HFH)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HFH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HFH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HFH)

(-) PROSITE Motifs  (3, 3)

NMR Structure (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FORK_HEAD_1PS00657 Fork head domain signature 1.FOXD3_RAT3-16  1A:3-16
2FORK_HEAD_3PS50039 Fork head domain profile.FOXD3_RAT3-97  1A:3-93
3FORK_HEAD_2PS00658 Fork head domain signature 2.FOXD3_RAT47-53  1A:47-53

(-) Exons   (0, 0)

(no "Exon" information available for 2HFH)

(-) 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:93
 aligned with FOXD3_RAT | Q63245 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:93
                                    10        20        30        40        50        60        70        80        90   
             FOXD3_RAT    1 LVKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPQSEDMFDNGSFL 93
               SCOP domains d2hfha_ A: Genesis                                                                            SCOP domains
               CATH domains 2hfhA00 A:1-93 'winged helix' repressor DNA binding domain                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhh........hhhhhhhhh...hhhh...hhhhhhhhhhhhhh................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --FORK_HEAD_3  PDB: A:3-93 UniProt: 3-97                                                      PROSITE (1)
                PROSITE (2) --FORK_HEAD_1   ------------------------------FORK_HE---------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  2hfh A  1 MVKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPQSEDMFDNGSFL 93
                                    10        20        30        40        50        60        70        80        90   

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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  (0, 0)

(no "Pfam Domain" information available for 2HFH)

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (FOXD3_RAT | Q63245)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000981    RNA polymerase II transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    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:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases 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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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.

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        FOXD3_RAT | Q632452hdc

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