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- PDB-2dms: Solution structure of the homeobox domain of Homeobox protein OTX2 -

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Basic information

Entry
Database: PDB / ID: 2dms
TitleSolution structure of the homeobox domain of Homeobox protein OTX2
ComponentsHomeobox protein OTX2
KeywordsDNA BINDING PROTEIN / homeobox domain / three helices with the DNA binding helix-turn-helix motif / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


eye photoreceptor cell fate commitment / diencephalon morphogenesis / metencephalon development / somite rostral/caudal axis specification / anatomical structure development / telencephalon regionalization / primitive streak formation / positive regulation of embryonic development / neuron fate determination / neuron fate commitment ...eye photoreceptor cell fate commitment / diencephalon morphogenesis / metencephalon development / somite rostral/caudal axis specification / anatomical structure development / telencephalon regionalization / primitive streak formation / positive regulation of embryonic development / neuron fate determination / neuron fate commitment / endoderm development / positive regulation of gastrulation / dopaminergic neuron differentiation / dorsal/ventral pattern formation / cell fate specification / anterior/posterior pattern specification / midbrain development / inner ear morphogenesis / oligodendrocyte differentiation / cell fate commitment / forebrain development / cellular response to leukemia inhibitory factor / central nervous system development / animal organ morphogenesis / axon guidance / neuron differentiation / sequence-specific double-stranded DNA binding / growth cone / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleus / cytoplasm
Similarity search - Function
Transcription factor Otx2 / Transcription factor Otx / Transcription factor Otx, C-terminal / Otx1 transcription factor / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Homeobox protein OTX2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsOhnishi, S. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the homeobox domain of Homeobox protein OTX2
Authors: Ohnishi, S. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionApr 24, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 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: Homeobox protein OTX2


Theoretical massNumber of molelcules
Total (without water)9,1141
Polymers9,1141
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 / 100target function, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Homeobox protein OTX2


Mass: 9114.188 Da / Num. of mol.: 1 / Fragment: homeobox domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: Otx2 / Plasmid: P050711-11 / Production host: Cell free synthesis / References: UniProt: P80206

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.0mM protein U-15N,13C; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.965Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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