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- PDB-3zob: Solution structure of chicken Engrailed 2 homeodomain -

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Basic information

Entry
Database: PDB / ID: 3zob
TitleSolution structure of chicken Engrailed 2 homeodomain
ComponentsHOMEOBOX PROTEIN ENGRAILED-2
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / CELL-PENETRATING PEPTIDE
Function / homology
Function and homology information


hindbrain development / embryonic brain development / dopaminergic neuron differentiation / midbrain development / positive regulation of phosphorylation / filopodium / axon guidance / positive regulation of translation / neuron differentiation / fibrillar center ...hindbrain development / embryonic brain development / dopaminergic neuron differentiation / midbrain development / positive regulation of phosphorylation / filopodium / axon guidance / positive regulation of translation / neuron differentiation / fibrillar center / lamellipodium / growth cone / negative regulation of neuron apoptotic process / DNA-binding transcription factor activity, RNA polymerase II-specific / neuron projection / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / 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. ...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 / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Homeobox protein engrailed-2
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsCarlier, L. / Balayssac, S. / Cantrelle, F.X. / Khemtemourian, L. / Chassaing, G. / Joliot, A. / Lequin, O.
CitationJournal: Biophys.J. / Year: 2013
Title: Investigation of Homeodomain Membrane Translocation Properties: Insights from the Structure Determination of Engrailed-2 Homeodomain in Aqueous and Membrane-Mimetic Environments.
Authors: Carlier, L. / Balayssac, S. / Cantrelle, F. / Khemtemourian, L. / Chassaing, G. / Joliot, A. / Lequin, O.
History
DepositionFeb 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 2.0May 15, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HOMEOBOX PROTEIN ENGRAILED-2


Theoretical massNumber of molelcules
Total (without water)7,8631
Polymers7,8631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein HOMEOBOX PROTEIN ENGRAILED-2 / GG-EN-2 / HOMEOBOX PROTEIN EN-2 / ENGRAILED 2 HOMEOPROTEIN


Mass: 7862.982 Da / Num. of mol.: 1 / Fragment: HOMEODOMAIN, RESIDUES 200-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RP / References: UniProt: Q05917

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N NOESY- HSQC
1313D 13C NOESY-HMQC
1413D HNHA
1513D HNHB
NMR detailsText: NONE

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Sample preparation

DetailsContents: 1 MM PROTEIN, 50 MM SODIUM SUCCINATE, 0.02% (W/V) SODIUM AZIDE, 0.1 MM TSP, 90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM / pH: 4.7 / Pressure: 1.0 atm / Temperature: 303.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
Xplor-NIHSCHWIETERS,KUSZEWSKI,TJrefinement
DYANAstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: ENERGY MINIMIZATION WITH CHARMM22 FORCE FIELD
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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