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(-) Description

Title :  STRUCTURE OF TRANSCRIPTION FACTOR GENESIS/DNA COMPLEX
 
Authors :  C. Jin, I. Marsden, X. Chen, X. Liao
Date :  05 May 99  (Deposition) - 05 Jul 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C  (20x)
Keywords :  Nmr, Structure, Dyanamics, Genesis, Winged Helix Protein, Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Jin, I. Marsden, X. Chen, X. Liao
Dynamic Dna Contacts Observed In The Nmr Structure Of Winged Helix Protein-Dna Complex.
J. Mol. Biol. V. 289 683 1999
PubMed-ID: 10369754  |  Reference-DOI: 10.1006/JMBI.1999.2819
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (TRANSCRIPTION FACTOR)
    Chains: A
    Engineered: YES
    Fragment: DNA BINDING DOMAIN
    Gene: GENESIS
    Organelle: NUCLEUS
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
 
Molecule 2 - DNA (5'- D(P*GP*CP*TP*TP*AP*AP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*C)-3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(P*GP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*TP*TP*AP*AP*GP*C)-3')
    Chains: C
    Engineered: YES
    Synthetic: YES

 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 2HDC)

(-) Sites  (0, 0)

(no "Site" information available for 2HDC)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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:3-97
3FORK_HEAD_2PS00658 Fork head domain signature 2.FOXD3_RAT47-53  1A:47-53

(-) Exons   (0, 0)

(no "Exon" information available for 2HDC)

(-) 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:97
 aligned with FOXD3_RAT | Q63245 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:97
                                    11        21        31        41        51        61        71        81        91       
            FOXD3_RAT     2 VKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPQSEDMFDNGSFLRRRKR  98
               SCOP domains d2hdca_ A: Genesis                                                                                SCOP domains
               CATH domains 2hdcA00 A:2-98 'winged helix' repressor DNA binding domain                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.eee...........eee...hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -FORK_HEAD_3  PDB: A:3-97 UniProt: 3-97                                                         - PROSITE (1)
                PROSITE (2) -FORK_HEAD_1   ------------------------------FORK_HE--------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 2hdc A   2 VKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPQSEDMFDNGSFLRRRKR  98
                                    11        21        31        41        51        61        71        81        91       


Chain B from PDB  Type:DNA  Length:17
                                                 
                 2hdc B 249 GCTTAAAATAACAATAC 265
                                   258       


Chain C from PDB  Type:DNA  Length:17
                                                 
                 2hdc C 349 GTATTGTTATTTTAAGC 365
                                   358
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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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) 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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 Related Entries

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        FOXD3_RAT | Q63245: 2hfh

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