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(-) Description

Title :  EVEN-SKIPPED HOMEODOMAIN COMPLEXED TO AT-RICH DNA
 
Authors :  J. A. Hirsch, A. K. Aggarwal
Date :  25 Jun 01  (Deposition) - 06 Jul 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Even-Skipped, Homeodomain, Protein-Dna Complex, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. A. Hirsch, A. K. Aggarwal
Structure Of The Even-Skipped Homeodomain Complexed To At-Rich Dna: New Perspectives On Homeodomain Specificity.
Embo J. V. 14 6280 1995
PubMed-ID: 8557047
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(P*TP*AP*AP*TP*TP*GP*AP*AP*TP*T)-3'
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 2 - 5'-D(P*AP*AP*TP*TP*CP*AP*AP*TP*TP*A)-3'
    ChainsD
    EngineeredYES
    SyntheticYES
 
Molecule 3 - SEGMENTATION PROTEIN EVEN-SKIPPED
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-3A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentHOMEODOMAIN
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1JGG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_1PS00027 'Homeobox' domain signature.EVE_DROME103-126
 
  2A:134-157
B:334-357

(-) Exons   (0, 0)

(no "Exon" information available for 1JGG)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:57
 aligned with EVE_DROME | P06602 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:57
                                    81        91       101       111       121       
            EVE_DROME    72 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 128
               SCOP domains d1jgga_ A: Even-skipped homeodomain                       SCOP domains
               CATH domains 1jggA00 A:103-159 Homeodomain-like                        CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------HOMEOBOX_1              -- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                 1jgg A 103 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 159
                                   112       122       132       142       152       

Chain B from PDB  Type:PROTEIN  Length:57
 aligned with EVE_DROME | P06602 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:57
                                    81        91       101       111       121       
            EVE_DROME    72 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 128
               SCOP domains d1jggb_ B: Even-skipped homeodomain                       SCOP domains
               CATH domains 1jggB00 B:303-359 Homeodomain-like                        CATH domains
           Pfam domains (1) Homeobox-1jggB01 B:303-358                              - Pfam domains (1)
           Pfam domains (2) Homeobox-1jggB02 B:303-358                              - Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------HOMEOBOX_1              -- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                 1jgg B 303 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 359
                                   312       322       332       342       352       

Chain C from PDB  Type:DNA  Length:10
                                          
                 1jgg C 201 TAATTGAATT 210
                                   210

Chain D from PDB  Type:DNA  Length:10
                                          
                 1jgg D 211 AATTCAATTA 220
                                   220

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (EVE_DROME | P06602)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000980    RNA polymerase II distal enhancer sequence-specific DNA binding    Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
    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:0003705    transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
    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:0007512    adult heart development    The process whose specific outcome is the progression of the adult heart over time, from its formation to the mature structure.
    GO:0008595    anterior/posterior axis specification, embryo    The specification of the anterior/posterior axis of the embryo by the products of genes expressed maternally and genes expressed in the zygote.
    GO:0007350    blastoderm segmentation    The hierarchical steps resulting in the progressive subdivision of the anterior/posterior axis of the embryo.
    GO:0045165    cell fate commitment    The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.
    GO:0001709    cell fate determination    A process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    GO:0007376    cephalic furrow formation    Formation of a partial necklace of inturning tissue on the lateral sides of the embryo, along the dorsal-ventral axis. This furrow demarcates head from thorax in the developing protostome.
    GO:0007377    germ-band extension    Elongation of the germ band on the ventral side of the embryo, accompanied by a halving in width. The elongation process pushes the posterior midgut invagination closed and compresses the amnioserosa further.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0003007    heart morphogenesis    The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0008045    motor neuron axon guidance    The process in which the migration of an axon growth cone of a motor neuron is directed to a specific target site in response to a combination of attractive and repulsive cues.
    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:0007517    muscle organ development    The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
    GO:0009997    negative regulation of cardioblast cell fate specification    Any process that restricts, stops or prevents a cell from specifying into a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating.
    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:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0007366    periodic partitioning by pair rule gene    Allocation of cells to parasegments in the embryo, through the action of overlapping series of pair rule gene activities.
    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:0035289    posterior head segmentation    Partitioning the posterior region of the insect head anlage into gnathal (mandibular, maxillary and labial) segments. Unlike the anterior head (procephalic) segments, formation of the posterior head (gnathal) segments occurs by a similar mechanism to trunk segmentation, where a cascade of gap genes, pair-rule genes and segment-polarity genes subdivide the embryo into progressively smaller domains.
    GO:0050770    regulation of axonogenesis    Any process that modulates the frequency, rate or extent of axonogenesis, the generation of an axon, the long process of a neuron.
    GO:1901739    regulation of myoblast fusion    Any process that modulates the frequency, rate or extent of myoblast fusion.
    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.
    GO:0035290    trunk segmentation    Partitioning of the blastoderm embryo into trunk segmental units. In Drosophila, the trunk segments include thoracic segments and abdominal segments A1 to A8.
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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