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- PDB-2ff0: Solution Structure of Steroidogenic Factor 1 DNA Binding Domain B... -
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Basic information
Entry | Database: PDB / ID: 2ff0 | ||||||
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Title | Solution Structure of Steroidogenic Factor 1 DNA Binding Domain Bound to its Target Sequence in the Inhibin alpha-subunit Promoter | ||||||
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![]() | Hormone/Growth factor/DNA / Nuclear Hormone Receptor / Protein-DNA complex / Monomeric Receptor-DNA complex / Hormone-Growth factor-DNA COMPLEX | ||||||
Function / homology | ![]() response to gonadotropin-releasing hormone / Sertoli cell differentiation / SUMOylation of intracellular receptors / negative regulation of female gonad development / Nuclear Receptor transcription pathway / sex determination / positive regulation of male gonad development / calcineurin-mediated signaling / luteinization / tissue development ...response to gonadotropin-releasing hormone / Sertoli cell differentiation / SUMOylation of intracellular receptors / negative regulation of female gonad development / Nuclear Receptor transcription pathway / sex determination / positive regulation of male gonad development / calcineurin-mediated signaling / luteinization / tissue development / Leydig cell differentiation / male sex determination / maintenance of protein location in nucleus / hormone metabolic process / adrenal gland development / female gonad development / hormone-mediated signaling pathway / transcription coregulator binding / phospholipid binding / RNA polymerase II transcription regulator complex / nuclear receptor activity / male gonad development / double-stranded DNA binding / sequence-specific DNA binding / transcription by RNA polymerase II / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / Simulated annealing, cartesian molecular dynamics | ||||||
![]() | Little, T.H. / Zhang, Y. / Matulis, C.K. / Weck, J. / Zhang, Z. / Ramachandran, A. / Mayo, K.E. / Radhakrishnan, I. | ||||||
![]() | ![]() Title: Sequence-specific deoxyribonucleic Acid (DNA) recognition by steroidogenic factor 1: a helix at the carboxy terminus of the DNA binding domain is necessary for complex stability. Authors: Little, T.H. / Zhang, Y. / Matulis, C.K. / Weck, J. / Zhang, Z. / Ramachandran, A. / Mayo, K.E. / Radhakrishnan, I. | ||||||
History |
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Remark 650 | HELIX AUTHOR DETERMINED HELIX RECORDS BASED ON PROCHECK OUTPUT OF ENTIRE NMR ENSEMBLE |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 821 KB | Display | ![]() |
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PDB format | ![]() | 677.7 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: 4620.000 Da / Num. of mol.: 1 / Fragment: Inhibin Alpha-Subunit Promoter / Source method: obtained synthetically Details: The DNA sequence was synthesized via automated methods |
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#2: DNA chain | Mass: 4561.947 Da / Num. of mol.: 1 / Fragment: Inhibin Alpha-Subunit Promoter / Source method: obtained synthetically Details: The DNA sequence was synthesized via automated methods |
#3: Protein | Mass: 11890.955 Da / Num. of mol.: 1 / Fragment: DNA Binding Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details |
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Sample conditions | Ionic strength: 20 mM Tris acetate, 50 uM ZnCl2, 2 mM DTT, 1% glycerol pH: 6 / Pressure: ambient / Temperature: 308 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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Processing
NMR software |
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Refinement | Method: Simulated annealing, cartesian molecular dynamics / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: best captures the intermolecular interactions observed in the ensemble | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: lowest restraint energies, restraint violations, and RMS deviations from ideal covalent geometry Conformers calculated total number: 200 / Conformers submitted total number: 16 |