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- PDB-1omq: Structure of penetratin in bicellar solution -

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Basic information

Entry
Database: PDB / ID: 1omq
TitleStructure of penetratin in bicellar solution
ComponentsHomeotic antennapedia protein
KeywordsDNA BINDING PROTEIN / unstructured at the terminals / alpha helical in the middle
Function / homology
Function and homology information


specification of segmental identity, antennal segment / specification of segmental identity, thorax / neuroblast development / muscle cell fate specification / lymph gland development / ventral cord development / anterior/posterior axis specification / anterior/posterior pattern specification / midgut development / regulation of neurogenesis ...specification of segmental identity, antennal segment / specification of segmental identity, thorax / neuroblast development / muscle cell fate specification / lymph gland development / ventral cord development / anterior/posterior axis specification / anterior/posterior pattern specification / midgut development / regulation of neurogenesis / heart development / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
Homeobox protein, antennapedia type / Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Homeotic protein antennapedia
Similarity search - Component
MethodSOLUTION NMR / distance geometry
AuthorsLindberg, M. / Biverstahl, H. / Graslund, A. / Maler, L.
CitationJournal: Eur.J.Biochem. / Year: 2003
Title: Structure and positioning comparison of two variants of penetratin in two different membrane mimicking systems by NMR
Authors: Lindberg, M. / Biverstahl, H. / Graslund, A. / Maler, L.
History
DepositionFeb 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homeotic antennapedia protein


Theoretical massNumber of molelcules
Total (without water)2,2541
Polymers2,2541
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60structures with the lowest energy
RepresentativeModel #1closest to the average,lowest energy

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Components

#1: Protein/peptide Homeotic antennapedia protein / penetratin


Mass: 2253.781 Da / Num. of mol.: 1 / Fragment: C-terminal fragment / Source method: obtained synthetically
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.
References: UniProt: P02833

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
NMR detailsText: Structure was determined by standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 3mM penetratin, 50 mM KCl; 15% w/v (DMPC+DMPG)/DHPC bicellar solution with q=0.5 and 5% D2O
Solvent system: 15% w/v (DMPC+DMPG)/DHPC bicellar solution with q=0.5 and 5% D2O
Sample conditionsIonic strength: 50mM KCl / pH: 5.5 / Pressure: 1 atm / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1ccollection
Felix2000.1data analysis
DYANA1.5Guntert, Mumenthaler, Herrmannstructure solution
DYANA1.5Guntert, Mumenthaler, Herrmannrefinement
RefinementMethod: distance geometry / Software ordinal: 1
Details: A total of 129 distance constraints where identified, mostly sequential and medium range NOEs (40 intra-residue, 54 sequential and 35 medium range NOEs)
NMR representativeSelection criteria: closest to the average,lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 20

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