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- PDB-1mdm: INHIBITED FRAGMENT OF ETS-1 AND PAIRED DOMAIN OF PAX5 BOUND TO DNA -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mdm | ||||||
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Title | INHIBITED FRAGMENT OF ETS-1 AND PAIRED DOMAIN OF PAX5 BOUND TO DNA | ||||||
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![]() | TRANSCRIPTION/DNA / Transcription factor / ternary complex / autoinhibition / ETS domain / Paired domain / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | ![]() RUNX1 regulates transcription of genes involved in BCR signaling / Oncogene Induced Senescence / lateral ventricle development / regulation of extracellular matrix disassembly / embryonic cranial skeleton morphogenesis / adult behavior / histone acetyltransferase binding / immune system process / skeletal muscle cell differentiation / regulation of angiogenesis ...RUNX1 regulates transcription of genes involved in BCR signaling / Oncogene Induced Senescence / lateral ventricle development / regulation of extracellular matrix disassembly / embryonic cranial skeleton morphogenesis / adult behavior / histone acetyltransferase binding / immune system process / skeletal muscle cell differentiation / regulation of angiogenesis / positive regulation of endothelial cell migration / B cell differentiation / positive regulation of erythrocyte differentiation / cerebral cortex development / negative regulation of inflammatory response / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / nucleic acid binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Garvie, C.W. / Pufall, M.A. / Graves, B.J. / Wolberger, C. | ||||||
![]() | ![]() Title: STRUCTURAL ANALYSIS OF THE AUTOINHIBITION OF ETS-1 AND ITS ROLE IN PROTEIN PARTNERSHIPS Authors: Garvie, C.W. / Pufall, M.A. / Graves, B.J. / Wolberger, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.8 KB | Display | ![]() |
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PDB format | ![]() | 62.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.7 KB | Display | ![]() |
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Full document | ![]() | 469.5 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 19.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1md0C ![]() 1k78S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 8036.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesised by the phosphoramidite method |
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#2: DNA chain | Mass: 7943.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesised by the phosphoramidite method |
#3: Protein | Mass: 16653.172 Da / Num. of mol.: 1 / Fragment: PAIRED DNA-BINDING DOMAIN, RESIDUES 1-149 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 18678.154 Da / Num. of mol.: 1 Fragment: INHIBITED ETS DNA-BINDING DOMAIN, RESIDUES 280-440 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.73 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 200mM Ammonium Acetate, 10% Peg4000, 100mM Acetate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 13, 2001 / Details: mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→40 Å / Num. all: 39863 / Num. obs: 13405 / % possible obs: 87.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.5 / Redundancy: 3.1 % / Biso Wilson estimate: 84.6 Å2 / Rsym value: 0.06 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 4 / Num. unique all: 2937 / Rsym value: 0.116 / % possible all: 58.7 |
Reflection | *PLUS Lowest resolution: 35 Å / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 58.7 % / Rmerge(I) obs: 0.192 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ID 1K78 Resolution: 2.8→32.03 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The side chains for the region 88-141 of Pax5 are included in the model despite a lack of electron density to uniquely define their location. The poor definition of the amino acid sidechains ...Details: The side chains for the region 88-141 of Pax5 are included in the model despite a lack of electron density to uniquely define their location. The poor definition of the amino acid sidechains in this region of Pax5 reflects the loss of contacts to the sugar-phosphate backbone, due to the less than optimal length of the DNA sequence used. This may explain the high B-factors obtained overall for the structure. The electron density for the side chains of residues in the region between residues 309-318 in Ets-1 was poorly defined and only the side chains for Arg309, Asp310 and Leu314 could be built.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 21.8329 Å2 / ksol: 0.276781 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→32.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 35 Å / Rfactor Rfree: 0.31 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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