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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 | ||||||
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Title | NMR Solution Structure of the Bicoid Homeodomain Bound to the Consensus DNA Binding Site TAATCC | ||||||
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![]() | TRANSCRIPTION/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 | ![]() 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 / negative regulation of translation ...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 / negative regulation of translation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION 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) | ||||||
![]() | Baird-Titus, J.M. / Rance, M. / Clark-Baldwin, K. / Ma, J. / Vrushank, D. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 825.7 KB | Display | ![]() |
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PDB format | ![]() | 639 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: DNA chain | Mass: 3887.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CONSENSUS DNA BINDING SITE SENSE STRAND |
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#2: DNA chain | Mass: 4056.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CONSENSUS DNA BINDING SITE ANTI-SENSE STRAND |
#3: Protein | Mass: 7963.067 Da / Num. of mol.: 1 / Fragment: Homeodomain (residues 97-163) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 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 |
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Sample conditions | pH: 7 / Pressure: 1 atm / Temperature: 295 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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Processing
NMR software |
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Refinement | 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 - ...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 representative | Selection criteria: closest to the average | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |