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Open data
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Basic information
Entry | Database: PDB / ID: 5ef6 | ||||||
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Title | Structure of HOXB13 complex with methylated DNA | ||||||
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![]() | TRANSCRIPTION / transcription factor / methylated DNA / complex | ||||||
Function / homology | ![]() epithelial cell maturation involved in prostate gland development / methyl-CpG binding / regulation of growth / response to testosterone / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epidermis development / DNA-binding transcription repressor activity, RNA polymerase II-specific / response to wounding / sequence-specific double-stranded DNA binding / angiogenesis ...epithelial cell maturation involved in prostate gland development / methyl-CpG binding / regulation of growth / response to testosterone / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epidermis development / DNA-binding transcription repressor activity, RNA polymerase II-specific / response to wounding / sequence-specific double-stranded DNA binding / angiogenesis / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Morgunova, E. / Yin, Y. / Jolma, A. / Popov, A. / Taipale, J. | ||||||
![]() | ![]() Title: Impact of cytosine methylation on DNA binding specificities of human transcription factors. Authors: Yin, Y. / Morgunova, E. / Jolma, A. / Kaasinen, E. / Sahu, B. / Khund-Sayeed, S. / Das, P.K. / Kivioja, T. / Dave, K. / Zhong, F. / Nitta, K.R. / Taipale, M. / Popov, A. / Ginno, P.A. / ...Authors: Yin, Y. / Morgunova, E. / Jolma, A. / Kaasinen, E. / Sahu, B. / Khund-Sayeed, S. / Das, P.K. / Kivioja, T. / Dave, K. / Zhong, F. / Nitta, K.R. / Taipale, M. / Popov, A. / Ginno, P.A. / Domcke, S. / Yan, J. / Schubeler, D. / Vinson, C. / Taipale, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.5 KB | Display | ![]() |
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PDB format | ![]() | 109.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 500.6 KB | Display | ![]() |
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Full document | ![]() | 510.2 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 24.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5egoC ![]() 5hodC ![]() 5ltyC ![]() 5luxC ![]() 5ednS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 7510.880 Da / Num. of mol.: 4 / Fragment: UNP residues 217-278 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | Mass: 5542.600 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 5516.636 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 3350, potassium chloride, magnesium chloride, 2-methyl-1-propanol, Tris PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 26, 2015 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.98→55.16 Å / Num. all: 17811 / Num. obs: 17019 / % possible obs: 97.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 36.6 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.13 / Rrim(I) all: 0.241 / Net I/σ(I): 5 / Num. measured all: 57890 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5edn Resolution: 3→38.169 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 40.45 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 145.57 Å2 / Biso mean: 41.4815 Å2 / Biso min: 4.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→38.169 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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