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(-) Description

Title :  STRUCTURE OF PENETRATIN IN BICELLAR SOLUTION
 
Authors :  M. Lindberg, H. Biverstahl, A. Graslund, L. Maler
Date :  26 Feb 03  (Deposition) - 29 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Unstructured At The Terminals, Alpha Helical In The Middle, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Lindberg, H. Biverstahl, A. Graslund, L. Maler
Structure And Positioning Comparison Of Two Variants Of Penetratin In Two Different Membrane Mimicking Systems By Nmr
Eur. J. Biochem. V. 270 3055 2003
PubMed-ID: 12846839  |  Reference-DOI: 10.1046/J.1432-1033.2003.03685.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HOMEOTIC ANTENNAPEDIA PROTEIN
    Chains: A
    Engineered: YES
    Fragment: C-TERMINAL FRAGMENT
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN DROSOPHILA MELANOGASTER (FRUIT FLY). THE PEPTIDE WAS OBTAINED FROM NEOSYSTEM INC. AND USED WITHOUT FURTHER PURIFICATION.
    Synonym: PENETRATIN
    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 1OMQ)

(-) Sites  (0, 0)

(no "Site" information available for 1OMQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OMQ)

(-) Exons   (0, 0)

(no "Exon" information available for 1OMQ)

(-) 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:16
 aligned with ANTP_DROME | P02833 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:16
                                   348      
           ANTP_DROME   339 RQIKIWFQNRRMKWKK 354
               SCOP domains d1omqa_ A:       SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 1omq A  43 RQIKIWFQNRRMKWKK  58
                                    52
   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
(-)
Class: Peptides (792)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1OMQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1OMQ)

(-) Gene Ontology  (20, 20)

NMR Structure(hide GO term definitions)
Chain A   (ANTP_DROME | P02833)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0009948    anterior/posterior axis specification    The establishment, maintenance and elaboration of the anterior/posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
    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:0048542    lymph gland development    The process whose specific outcome is the progression of the lymph gland over time, from its formation to the mature structure. The lymph gland is one of the sites of hemocyte differentiation. It consists of three to six bilaterally paired lobes that are attached to the cardioblasts during larval stages, and it degenerates during pupal stages.
    GO:0007494    midgut development    The process whose specific outcome is the progression of the midgut over time, from its formation to the mature structure. The midgut is the middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine.
    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:0042694    muscle cell fate specification    The process in which a cell becomes capable of differentiating autonomously into a muscle cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed.
    GO:0014019    neuroblast development    The process aimed at the progression of a neuroblast over time, from initial commitment of the cell to a specific state, to the mature neuroblast. It does not include processes where the neuroblast turns into a glial cell or a neuron.
    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: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:0007379    segment specification    The process in which segments assume individual identities; exemplified in insects by the actions of the products of the homeotic genes.
    GO:0007383    specification of segmental identity, antennal segment    The specification of the characteristic structures of the antennal segment following establishment of segment boundaries. Identity is considered to be the aggregate of characteristics by which a structure is recognized.
    GO:0007384    specification of segmental identity, thorax    The specification of the characteristic structures of the thoracic segments following establishment of segment boundaries. Identity is considered to be the aggregate of characteristics by which a structure is recognized.
    GO:0007419    ventral cord development    The process whose specific outcome is the progression of the ventral cord over time, from its formation to the mature structure. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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

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

UniProtKB/Swiss-Prot
        ANTP_DROME | P02833: 1ahd 1hom 1kz0 1kz5 1san 2hoa 2nd6 2nd7 2nd8 4xic 4xid 5jlw 5jlx 9ant

(-) Related Entries Specified in the PDB File

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