+Open data
-Basic information
Entry | Database: PDB / ID: 2ypb | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the SCL:E47 complex bound to DNA | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / HEMATOPOIESIS / LEUKEMIA | ||||||
Function / homology | Function and homology information hemangioblast cell differentiation / regulation of mast cell differentiation / positive regulation of chromatin organization / astrocyte fate commitment / vitamin D response element binding / basophil differentiation / spinal cord association neuron differentiation / regulation of somatic stem cell population maintenance / megakaryocyte differentiation / bHLH transcription factor binding ...hemangioblast cell differentiation / regulation of mast cell differentiation / positive regulation of chromatin organization / astrocyte fate commitment / vitamin D response element binding / basophil differentiation / spinal cord association neuron differentiation / regulation of somatic stem cell population maintenance / megakaryocyte differentiation / bHLH transcription factor binding / immunoglobulin V(D)J recombination / mitogen-activated protein kinase kinase kinase binding / definitive hemopoiesis / embryonic hemopoiesis / megakaryocyte development / platelet formation / B cell lineage commitment / Myogenesis / erythrocyte maturation / E-box binding / regulation of G1/S transition of mitotic cell cycle / hemopoiesis / positive regulation of cell division / hematopoietic stem cell differentiation / cell fate commitment / cis-regulatory region sequence-specific DNA binding / positive regulation of cell cycle / positive regulation of B cell proliferation / positive regulation of neuron differentiation / B cell differentiation / positive regulation of mitotic cell cycle / erythrocyte differentiation / positive regulation of erythrocyte differentiation / locomotory behavior / positive regulation of DNA-binding transcription factor activity / positive regulation of protein-containing complex assembly / euchromatin / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / regulation of cell population proliferation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å | ||||||
Authors | El Omari, K. / Hoosdally, S.J. / Tuladhar, K. / Karia, D. / Ponsele, E. / Platonova, O. / Vyas, P. / Patient, R. / Porcher, C. / Mancini, E.J. | ||||||
Citation | Journal: Cell Rep. / Year: 2013 Title: Structural Basis for Lmo2-Driven Recruitment of the Scl:E47bHLH Heterodimer to Hematopoietic-Specific Transcriptional Targets. Authors: El Omari, K. / Hoosdally, S.J. / Tuladhar, K. / Karia, D. / Hall-Ponsele, E. / Platonova, O. / Vyas, P. / Patient, R. / Porcher, C. / Mancini, E.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ypb.cif.gz | 101.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ypb.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ypb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ypb_validation.pdf.gz | 447.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ypb_full_validation.pdf.gz | 447.6 KB | Display | |
Data in XML | 2ypb_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 2ypb_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/2ypb ftp://data.pdbj.org/pub/pdb/validation_reports/yp/2ypb | HTTPS FTP |
-Related structure data
Related structure data | 2ypaSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 10721.119 Da / Num. of mol.: 1 / Fragment: BHLH, RESIDUES 5-78 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P17542 |
---|---|
#2: Protein | Mass: 9674.212 Da / Num. of mol.: 1 / Fragment: RESIDUES 535-613 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P15923 |
#3: DNA chain | Mass: 3284.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) |
#4: DNA chain | Mass: 3422.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 60 % / Description: NONE |
---|---|
Crystal grow | pH: 6 Details: 5 % (V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 40 MM MAGNESIUM CHLORIDE, 50 MM SODIUM CACODYLATE PH 6.0 AND 2MM GLUTATHIONE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→3 Å / Num. obs: 7203 / % possible obs: 97.8 % / Observed criterion σ(I): 1.2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.5 / % possible all: 98.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YPA Resolution: 2.87→42.44 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.937 / SU B: 51.981 / SU ML: 0.421 / Cross valid method: THROUGHOUT / ESU R: 1.563 / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 117.195 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.87→42.44 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|