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- PDB-1zq3: NMR Solution Structure of the Bicoid Homeodomain Bound to the Con... -

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Basic information

Entry
Database: PDB / ID: 1zq3
TitleNMR Solution Structure of the Bicoid Homeodomain Bound to the Consensus DNA Binding Site TAATCC
Components
  • 5'-D(*CP*GP*GP*GP*GP*AP*TP*TP*AP*GP*AP*GP*C)-3'
  • 5'-D(*GP*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*CP*G)-3'
  • Homeotic bicoid protein
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / HELIX-TURN-HELIX / HOMEODOMAIN / DNA-BINDING DOMAIN / K50 / RECOGNITION HELIX / TRANSCRIPTION FACTOR / TRANSLATIONAL CONTROL / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


anterior region determination / maternal determination of anterior/posterior axis, embryo / torso signaling pathway / segment polarity determination / anterior/posterior axis specification, embryo / anterior/posterior axis specification / oogenesis / translation repressor activity / mRNA 3'-UTR binding / sequence-specific DNA binding ...anterior region determination / maternal determination of anterior/posterior axis, embryo / torso signaling pathway / segment polarity determination / anterior/posterior axis specification, embryo / anterior/posterior axis specification / oogenesis / translation repressor activity / mRNA 3'-UTR binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of translation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
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) / Homeotic protein bicoid / Homeotic protein bicoid
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / protein structure - fast torsion angle dynamics algorithm (CYANA2.0), DNA structure - NUCGEN, simulated annealing with NMR-derived energy restraints (AMBER7.0), protein-DNA complex - simulated annealing with NMR-derived energy restraints (AMBER7.0), protein-DNA complex refinement - explicit solvent MD simulations (AMBER7.0)
AuthorsBaird-Titus, J.M. / Rance, M. / Clark-Baldwin, K. / Ma, J. / Vrushank, D.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site.
Authors: Baird-Titus, J.M. / Clark-Baldwin, K. / Dave, V. / Caperelli, C.A. / Ma, J. / Rance, M.
History
DepositionMay 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 / 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 / _struct_ref_seq_dif.details
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: 5'-D(*GP*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*CP*G)-3'
B: 5'-D(*CP*GP*GP*GP*GP*AP*TP*TP*AP*GP*AP*GP*C)-3'
P: Homeotic bicoid protein


Theoretical massNumber of molelcules
Total (without water)15,9073
Polymers15,9073
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 / 100structures with the lowest energy
RepresentativeModel #3closest to the average

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Components

#1: DNA chain 5'-D(*GP*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*CP*G)-3'


Mass: 3887.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CONSENSUS DNA BINDING SITE SENSE STRAND
#2: DNA chain 5'-D(*CP*GP*GP*GP*GP*AP*TP*TP*AP*GP*AP*GP*C)-3'


Mass: 4056.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CONSENSUS DNA BINDING SITE ANTI-SENSE STRAND
#3: Protein Homeotic bicoid protein / PRD-4


Mass: 7963.067 Da / Num. of mol.: 1 / Fragment: Homeodomain (residues 97-163)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: bcd / Plasmid: pET41a-Novagen / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star / References: UniProt: Q9UAM0, UniProt: P09081*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA
1412D NOESY

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Sample preparation

DetailsContents: 1mM Bicoid Homeodomain (15N/13C), 1mM Duplex DNA (unlabeled), 10mM phosphate buffer, pH 7.0, 1mM DTT, 1mM PMSF, 1mM EDTA, 1mM sodium azide, 0.3mM leupeptin, 0.2mM pefabloc (Roche), 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 7 / Pressure: 1 atm / Temperature: 295 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
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Peter Guntertstructure solution
Amber7D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, K.M. Merz, B. Wang, D.A. Pearlman, M. Crowley, S. Brozell, V. Tsui, H. Gohlke, J. Mongan, V. Hornak, G. Cui, P. Beroza, C. Schafmeister, J.W. Caldwell, W.S. Ross, and P.A. Kollman.refinement
Sparky3.109T. D. Goddard and D. G. Knellerdata analysis
NMRPipeF. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
RefinementMethod: protein structure - fast torsion angle dynamics algorithm (CYANA2.0), DNA structure - NUCGEN, simulated annealing with NMR-derived energy restraints (AMBER7.0), protein-DNA complex - ...Method: protein structure - fast torsion angle dynamics algorithm (CYANA2.0), DNA structure - NUCGEN, simulated annealing with NMR-derived energy restraints (AMBER7.0), protein-DNA complex - simulated annealing with NMR-derived energy restraints (AMBER7.0), protein-DNA complex refinement - explicit solvent MD simulations (AMBER7.0)
Software ordinal: 1
Details: 1724 total restraints used, 1076 protein distance restraints(NOESY), 34 protein hydrogen bond restraints(3D NOESY ,i-i+4), 134 angle restraints(HNHA), 192 DNA distance restraints(2D NOESY), ...Details: 1724 total restraints used, 1076 protein distance restraints(NOESY), 34 protein hydrogen bond restraints(3D NOESY ,i-i+4), 134 angle restraints(HNHA), 192 DNA distance restraints(2D NOESY), 55 watson-crick restraints(B-DNA), 200 DNA angle restraints(B-DNA), 33 protein-DNA distance restraints (2D NOESY)
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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