+Open data
-Basic information
Entry | Database: PDB / ID: 6mgn | ||||||
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Title | mouse Id1 (51-104) - human hE47 (348-399) complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / DNA-binding protein inhibitor ID-1 / transcription factor E2-alpha isoform E47 [Homo sapiens] | ||||||
Function / homology | Function and homology information regulation of vasculature development / negative regulation of endothelial cell differentiation / Oncogene Induced Senescence / negative regulation of dendrite morphogenesis / bHLH transcription factor binding / lung vasculature development / collagen metabolic process / positive regulation of actin filament bundle assembly / endothelial cell morphogenesis / immunoglobulin V(D)J recombination ...regulation of vasculature development / negative regulation of endothelial cell differentiation / Oncogene Induced Senescence / negative regulation of dendrite morphogenesis / bHLH transcription factor binding / lung vasculature development / collagen metabolic process / positive regulation of actin filament bundle assembly / endothelial cell morphogenesis / immunoglobulin V(D)J recombination / vitamin D response element binding / endothelial cell apoptotic process / mitogen-activated protein kinase kinase kinase binding / transcription regulator inhibitor activity / negative regulation of cold-induced thermogenesis / proteasome binding / B cell lineage commitment / lung morphogenesis / Myogenesis / E-box binding / regulation of G1/S transition of mitotic cell cycle / regulation of MAPK cascade / negative regulation of osteoblast differentiation / regulation of angiogenesis / cis-regulatory region sequence-specific DNA binding / BMP signaling pathway / negative regulation of endothelial cell apoptotic process / positive regulation of cell cycle / positive regulation of B cell proliferation / positive regulation of neuron differentiation / B cell differentiation / positive regulation of epithelial cell proliferation / circadian regulation of gene expression / protein destabilization / euchromatin / positive regulation of DNA-binding transcription factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / circadian rhythm / RNA polymerase II transcription regulator complex / : / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nervous system development / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / cell differentiation / protein dimerization activity / 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 / negative regulation of gene expression / response to antibiotic / negative regulation of DNA-templated transcription / centrosome / apoptotic process / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / 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 / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å | ||||||
Authors | Benezra, R. / Pavletich, N.P. / Gall, A.-L. / Goldgur, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell Rep / Year: 2019 Title: A Small-Molecule Pan-Id Antagonist Inhibits Pathologic Ocular Neovascularization. Authors: Wojnarowicz, P.M. / Lima E Silva, R. / Ohnaka, M. / Lee, S.B. / Chin, Y. / Kulukian, A. / Chang, S.H. / Desai, B. / Garcia Escolano, M. / Shah, R. / Garcia-Cao, M. / Xu, S. / Kadam, R. / ...Authors: Wojnarowicz, P.M. / Lima E Silva, R. / Ohnaka, M. / Lee, S.B. / Chin, Y. / Kulukian, A. / Chang, S.H. / Desai, B. / Garcia Escolano, M. / Shah, R. / Garcia-Cao, M. / Xu, S. / Kadam, R. / Goldgur, Y. / Miller, M.A. / Ouerfelli, O. / Yang, G. / Arakawa, T. / Albanese, S.K. / Garland, W.A. / Stoller, G. / Chaudhary, J. / Norton, L. / Soni, R.K. / Philip, J. / Hendrickson, R.C. / Iavarone, A. / Dannenberg, A.J. / Chodera, J.D. / Pavletich, N. / Lasorella, A. / Campochiaro, P.A. / Benezra, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mgn.cif.gz | 38.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mgn.ent.gz | 25 KB | Display | PDB format |
PDBx/mmJSON format | 6mgn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mgn_validation.pdf.gz | 419.2 KB | Display | wwPDB validaton report |
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Full document | 6mgn_full_validation.pdf.gz | 419.4 KB | Display | |
Data in XML | 6mgn_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 6mgn_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/6mgn ftp://data.pdbj.org/pub/pdb/validation_reports/mg/6mgn | HTTPS FTP |
-Related structure data
Related structure data | 6mgmC 6u2uC 5t9o S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 6142.190 Da / Num. of mol.: 1 / Fragment: unp residues 558-609 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TCF3, BHLHB21, E2A, ITF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P15923 |
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#2: Protein/peptide | Mass: 5584.515 Da / Num. of mol.: 1 / Fragment: unp residues 59-104 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Id1, Id, Id-1, Idb1 / Production host: Escherichia coli (E. coli) / References: UniProt: P20067 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.38 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M potassium phosphate (pH 6.0), 0.25 M NaCl, 22.5% PEG8000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.92 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 3, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 10249 / % possible obs: 98.7 % / Redundancy: 7 % / Rpim(I) all: 0.026 / Rsym value: 0.064 / Net I/σ(I): 29.3 |
Reflection shell | Resolution: 1.9→2 Å / Rsym value: 0.317 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5T9O 5t9o Resolution: 1.901→19.432 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.901→19.432 Å
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Refine LS restraints |
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LS refinement shell |
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