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(-) Description

Title :  SOLUTION NMR STRUCTURE OF THE GAGA FACTOR/DNA COMPLEX, REGULARIZED MEAN STRUCTURE
 
Authors :  G. M. Clore, J. G. Omichinski, A. M. Gronenborn
Date :  31 Dec 96  (Deposition) - 31 Dec 97  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C
Keywords :  Complex (Dna-Binding Protein/Dna), Chromatin Remodeling, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. G. Omichinski, P. V. Pedone, G. Felsenfeld, A. M. Gronenborn, G. M. Clore
The Solution Structure Of A Specific Gaga Factor-Dna Complex Reveals A Modular Binding Mode.
Nat. Struct. Biol. V. 4 122 1997
PubMed-ID: 9033593  |  Reference-DOI: 10.1038/NSB0297-122
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*GP*CP*CP*GP*AP*GP*AP*GP*TP*AP*C)-3')
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 2 - DNA (5'-D(*GP*TP*AP*CP*TP*CP*TP*CP*GP*GP*C)-3')
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 3 - GAGA-FACTOR
    ChainsA
    FragmentDNA BINDING DOMAIN, RESIDUES 310 - 372
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227

 Structural Features

(-) Chains, Units

  
NMR Structure 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:36 , CYS A:39 , HIS A:52 , HIS A:57BINDING SITE FOR RESIDUE ZN A 64

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.GAGA_DROME345-366  1A:36-57

(-) Exons   (0, 0)

(no "Exon" information available for 1YUI)

(-) 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:54
 aligned with GAGA_DROME | Q08605 from UniProtKB/Swiss-Prot  Length:581

    Alignment length:54
                                   328       338       348       358       368    
           GAGA_DROME   319 PKAKRAKHPPGTEKPRSRSQSEQPATCPICYAVIRQSRNLRRHLELRHFAKPGV 372
               SCOP domains d1yuia_ A: GAGA factor                                 SCOP domains
               CATH domains 1yuiA00 A:10-63 Classic Zinc Finger                    CATH domains
               Pfam domains GAGA-1yuiA01 A:10-63                                   Pfam domains
         Sec.struct. author ...............hhhh.....ee......ee..hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------ZINC_FINGER_C2H2_1    ------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                 1yui A  10 PKAKRAKHPPGTEKPRSRSQSEQPATCPICYAVIRQSRNLRRHLELRHFAKPGV  63
                                    19        29        39        49        59    

Chain B from PDB  Type:DNA  Length:11
                                           
                 1yui B 101 GCCGAGAGTAC 111
                                   110 

Chain C from PDB  Type:DNA  Length:11
                                           
                 1yui C 112 GTACTCTCGGC 122
                                   121 

   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  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: C2H2-zf (71)

(-) Gene Ontology  (37, 37)

NMR Structure(hide GO term definitions)
Chain A   (GAGA_DROME | Q08605)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0031208    POZ domain binding    Interacting selectively and non-covalently with a POZ (poxvirus and zinc finger) domain of a protein, a protein-protein interaction domain found in many transcription factors.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0031497    chromatin assembly    The assembly of DNA, histone proteins, other associated proteins, and sometimes RNA, into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus.
    GO:0006325    chromatin organization    Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
    GO:0007549    dosage compensation    Compensating for the variation in the unpaired sex chromosome:autosome chromosome ratios between sexes by activation or inactivation of genes on one or both of the sex chromosomes.
    GO:0007476    imaginal disc-derived wing morphogenesis    The process in which the anatomical structures of the imaginal disc-derived wing are generated and organized. The wing is an appendage modified for flying.
    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:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0000280    nuclear division    The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei.
    GO:0048477    oogenesis    The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
    GO:0031937    positive regulation of chromatin silencing    Any process that activates or increases the frequency, rate or extent of chromatin silencing.
    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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0051259    protein oligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates 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:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0035186    syncytial blastoderm mitotic cell cycle    Mitotic division cycles 10 to 13 of the insect embryo. This is the second phase of the syncytial period where nuclei divide in a common cytoplasm without cytokinesis. The majority of migrating nuclei reach the embryo surface during cycle 10, after which they divide less synchronously than before, and the syncytial blastoderm cycles lengthen progressively.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0000785    chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
    GO:0000791    euchromatin    A dispersed and relatively uncompacted form of chromatin.
    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:0005721    pericentric heterochromatin    Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.
    GO:0005700    polytene chromosome    A type of chromosome in a polyploid cell, formed when multiple copies of homologous chromosomes are aligned side by side to give a giant chromosome in which distinct chromosome bands are readily visible.

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 Related Entries

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

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        GAGA_DROME | Q086051yuj

(-) Related Entries Specified in the PDB File

1yuj ENSEMBLE OF 50 STRUCTURES