+
Open data
-
Basic information
Entry | Database: PDB / ID: 5ego | ||||||
---|---|---|---|---|---|---|---|
Title | HOXB13-MEIS1 heterodimer bound to methylated DNA | ||||||
![]() |
| ||||||
![]() | TRANSCRIPTION / transcription factor / heterodimer / complex / bound to DNA | ||||||
Function / homology | ![]() epithelial cell maturation involved in prostate gland development / cell growth involved in cardiac muscle cell development / negative regulation of myeloid cell differentiation / lens morphogenesis in camera-type eye / eye development / embryonic pattern specification / methyl-CpG binding / definitive hemopoiesis / regulation of growth / megakaryocyte development ...epithelial cell maturation involved in prostate gland development / cell growth involved in cardiac muscle cell development / negative regulation of myeloid cell differentiation / lens morphogenesis in camera-type eye / eye development / embryonic pattern specification / methyl-CpG binding / definitive hemopoiesis / regulation of growth / megakaryocyte development / response to testosterone / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / hemopoiesis / negative regulation of neuron differentiation / epidermis development / locomotory behavior / animal organ morphogenesis / brain development / DNA-binding transcription repressor activity, RNA polymerase II-specific / response to wounding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 binding / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 61.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 40.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 448.6 KB | Display | |
Data in XML | ![]() | 8.7 KB | Display | |
Data in CIF | ![]() | 10.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ef6C ![]() 5hodC ![]() 5ltyC ![]() 5luxC ![]() 4xrmS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 6756.834 Da / Num. of mol.: 1 / Fragment: UNP residues 279-333 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: DNA chain | Mass: 5600.653 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 5458.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Protein | Mass: 7640.061 Da / Num. of mol.: 1 / Fragment: UNP residues 217-277 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.72 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 5000, potassium chloride, magnesium chloride, Tris, PEG 400 PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 25, 2015 |
Radiation | Monochromator: Si(111) and Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→40 Å / Num. obs: 8290 / % possible obs: 98.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.54→2.63 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 1.6 / % possible all: 98.8 |
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4XRM Resolution: 2.54→38.544 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.45 / Stereochemistry target values: ML
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 164.57 Å2 / Biso mean: 70.1019 Å2 / Biso min: 49.36 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.54→38.544 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5401→2.9076 Å
|