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Open data
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Basic information
Entry | Database: PDB / ID: 4gfb | ||||||
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Title | Rap1/DNA complex | ||||||
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![]() | Transcription/DNA / double-Myb / Transcription-DNA complex | ||||||
Function / homology | ![]() positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / telomeric G-quadruplex DNA binding / protection from non-homologous end joining at telomere / establishment of protein localization to telomere / telomere maintenance via telomere lengthening / establishment of protein localization to chromatin / shelterin complex / double-stranded telomeric DNA binding / G-quadruplex DNA binding ...positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / telomeric G-quadruplex DNA binding / protection from non-homologous end joining at telomere / establishment of protein localization to telomere / telomere maintenance via telomere lengthening / establishment of protein localization to chromatin / shelterin complex / double-stranded telomeric DNA binding / G-quadruplex DNA binding / silent mating-type cassette heterochromatin formation / regulation of glycolytic process / DNA binding, bending / nucleosomal DNA binding / nuclear chromosome / telomeric DNA binding / TFIID-class transcription factor complex binding / subtelomeric heterochromatin formation / cis-regulatory region sequence-specific DNA binding / telomere maintenance / TBP-class protein binding / protein-DNA complex / histone binding / transcription regulator complex / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromosome, telomeric region / DNA-binding transcription factor activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Le Bihan, Y.-V. / Matot, B. / Le Du, M.-H. | ||||||
![]() | ![]() Title: Effect of Rap1 binding on DNA distortion and potassium permanganate hypersensitivity. Authors: Le Bihan, Y.V. / Matot, B. / Pietrement, O. / Giraud-Panis, M.J. / Gasparini, S. / Le Cam, E. / Gilson, E. / Sclavi, B. / Miron, S. / Le Du, M.H. #1: ![]() Title: The orientation of the C-terminal domain of the Saccharomyces cerevisiae Rap1 protein is determined by its binding to DNA. Authors: Matot, B. / Le Bihan, Y.-V. / Lescasse, R. / Perez, J. / Miron, S. / David, G. / Castaing, B. / Weber, P. / Raynal, B. / Zinn-Justin, S. / Gasparini, S. / Le Du, M.-H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.8 KB | Display | ![]() |
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PDB format | ![]() | 67.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453 KB | Display | ![]() |
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Full document | ![]() | 463.7 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ukgS 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: Protein | Mass: 31988.744 Da / Num. of mol.: 1 / Fragment: 358-596 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: RAP1, GRF1, TUF1, YNL216W, N1310 / Production host: ![]() ![]() |
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#2: DNA chain | Mass: 9398.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#3: DNA chain | Mass: 9668.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100mM Tris-HCl pH 8.0, 20% PEGmme-550, 100mM CaCl2, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→36.27 Å / Num. all: 12206 / Num. obs: 11279 / % possible obs: 92.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 66.52 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 16.61 |
Reflection shell | Resolution: 2.99→3.13 Å / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 3.1 / % possible all: 78.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3UKG Resolution: 2.99→36.27 Å / Cor.coef. Fo:Fc: 0.9152 / Cor.coef. Fo:Fc free: 0.8513 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 68.15 Å2
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Refine analyze | Luzzati coordinate error obs: 0.415 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.99→36.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.99→3.27 Å / Total num. of bins used: 6
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