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- PDB-2p81: Engrailed homeodomain helix-turn-helix motif -

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Basic information

Entry
Database: PDB / ID: 2p81
TitleEngrailed homeodomain helix-turn-helix motif
ComponentsSegmentation polarity homeobox protein engrailed
KeywordsTRANSCRIPTION / helix-turn-helix motif / motif / engrailed / homeodomain / DNA binding / protein folding / intermediate / native
Function / homology
Function and homology information


posterior compartment specification / analia development / anterior head segmentation / posterior head segmentation / anterior/posterior lineage restriction, imaginal disc / trunk segmentation / genital disc development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation ...posterior compartment specification / analia development / anterior head segmentation / posterior head segmentation / anterior/posterior lineage restriction, imaginal disc / trunk segmentation / genital disc development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation / wing disc morphogenesis / neuroblast fate determination / imaginal disc-derived wing vein specification / segment polarity determination / ventral midline development / compartment pattern specification / gonad development / RSC-type complex / RNA polymerase II transcription regulatory region sequence-specific DNA binding / axon guidance / neuron differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of gene expression / negative regulation of neuron apoptotic process / 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 gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Homeobox domain engrailed / Homeobox engrailed, C-terminal / Homeobox engrailed-type, conserved site / Engrailed homeobox C-terminal signature domain / 'Homeobox' engrailed-type protein signature. / Helix-turn-helix motif / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain ...Homeobox domain engrailed / Homeobox engrailed, C-terminal / Homeobox engrailed-type, conserved site / Engrailed homeobox C-terminal signature domain / 'Homeobox' engrailed-type protein signature. / Helix-turn-helix motif / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Segmentation polarity homeobox protein engrailed
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR
AuthorsReliga, T.L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: The helix-turn-helix motif as an ultrafast independently folding domain: The pathway of folding of Engrailed homeodomain.
Authors: Religa, T.L. / Johnson, C.M. / Vu, D.M. / Brewer, S.H. / Dyer, R.B. / Fersht, A.R.
History
DepositionMar 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Segmentation polarity homeobox protein engrailed


Theoretical massNumber of molelcules
Total (without water)5,4191
Polymers5,4191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Segmentation polarity homeobox protein engrailed


Mass: 5419.209 Da / Num. of mol.: 1 / Fragment: helix-turn-helix motif / Mutation: L16A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: en / Plasmid: pRSET A / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P02836

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY

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Sample preparation

DetailsContents: 500uM engrailed fragment 16-59, 50mM d-acetate, 100 mM NaCl, pH 5.7, 93%H2O / 7% D2O
Solvent system: 93% H2O/7% D2O
Sample conditionsIonic strength: 145mM / pH: 5.7 / Pressure: ambient / Temperature: 278 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeLast Update July 2, 2006Delaglioprocessing
Sparky3.106Goddartdata analysis
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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