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- PDB-2ld5: Solution NMR-derived complex structure of Hoxa13 DNA binding doma... -

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Basic information

Entry
Database: PDB / ID: 2ld5
TitleSolution NMR-derived complex structure of Hoxa13 DNA binding domain bound to DNA
Components
  • DNA (5'-D(*CP*AP*AP*AP*TP*AP*AP*AP*AP*TP*C)-3')
  • DNA (5'-D(P*GP*AP*TP*TP*TP*TP*AP*TP*TP*TP*G)-3')
  • Homeobox protein Hox-A13
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


endothelial cell fate specification / positive regulation of mesenchymal cell apoptotic process / embryonic hindgut morphogenesis / mitotic nuclear division / regulation of BMP signaling pathway / mesenchymal cell apoptotic process / branching involved in prostate gland morphogenesis / endothelial cell morphogenesis / tissue homeostasis / male genitalia development ...endothelial cell fate specification / positive regulation of mesenchymal cell apoptotic process / embryonic hindgut morphogenesis / mitotic nuclear division / regulation of BMP signaling pathway / mesenchymal cell apoptotic process / branching involved in prostate gland morphogenesis / endothelial cell morphogenesis / tissue homeostasis / male genitalia development / intermediate filament cytoskeleton / embryonic forelimb morphogenesis / artery morphogenesis / ventricular septum development / response to testosterone / inner ear development / anatomical structure morphogenesis / vasculogenesis / cis-regulatory region sequence-specific DNA binding / positive regulation of mitotic nuclear division / animal organ morphogenesis / chromosome / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription by RNA polymerase II / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Homeobox protein Hox1A3 N-terminal / : / Hox protein A13 N terminal / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like ...Homeobox protein Hox1A3 N-terminal / : / Hox protein A13 N terminal / 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
DNA / DNA (> 10) / Homeobox protein Hox-A13
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsZhang, Y.
CitationJournal: Plos One / Year: 2011
Title: Structural basis for sequence specific DNA binding and protein dimerization of HOXA13.
Authors: Zhang, Y. / Larsen, C.A. / Stadler, H.S. / Ames, J.B.
History
DepositionMay 14, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Apr 27, 2016Group: Structure summary
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / 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_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homeobox protein Hox-A13
B: DNA (5'-D(*CP*AP*AP*AP*TP*AP*AP*AP*AP*TP*C)-3')
C: DNA (5'-D(P*GP*AP*TP*TP*TP*TP*AP*TP*TP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)15,3743
Polymers15,3743
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)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Homeobox protein Hox-A13 / Homeobox protein Hox-1.10


Mass: 8670.194 Da / Num. of mol.: 1 / Fragment: Homeobox DNA binding residues 320-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hox-1.10, Hoxa13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q62424
#2: DNA chain DNA (5'-D(*CP*AP*AP*AP*TP*AP*AP*AP*AP*TP*C)-3')


Mass: 3334.239 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*GP*AP*TP*TP*TP*TP*AP*TP*TP*TP*G)-3')


Mass: 3369.217 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] sodium phosphate, 100% D2O
Solvent system: 100% D2O
SampleConc.: 0.5 mM / Component: sodium phosphate-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.025 / pH: 6 / Pressure: ambient / Temperature: 310 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
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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