+Open data
-Basic information
Entry | Database: PDB / ID: 4gfb | ||||||
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Title | Rap1/DNA complex | ||||||
Components |
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Keywords | Transcription/DNA / double-Myb / Transcription-DNA complex | ||||||
Function / homology | Function and homology information positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / protection from non-homologous end joining at telomere / establishment of protein localization to telomere / establishment of protein localization to chromatin / telomere maintenance via telomere lengthening / shelterin complex / G-quadruplex DNA binding / double-stranded telomeric DNA binding / silent mating-type cassette heterochromatin formation ...positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / protection from non-homologous end joining at telomere / establishment of protein localization to telomere / establishment of protein localization to chromatin / telomere maintenance via telomere lengthening / shelterin complex / G-quadruplex DNA binding / double-stranded telomeric DNA binding / silent mating-type cassette heterochromatin formation / regulation of glycolytic process / DNA binding, bending / nuclear chromosome / telomeric DNA binding / TFIID-class transcription factor complex binding / subtelomeric heterochromatin formation / cis-regulatory region sequence-specific DNA binding / nucleosomal DNA binding / TBP-class protein binding / telomere maintenance / protein-DNA complex / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / chromosome, telomeric region / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | ||||||
Authors | Le Bihan, Y.-V. / Matot, B. / Le Du, M.-H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 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: Journal: Nucleic Acids Res. / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gfb.cif.gz | 94.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gfb.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 4gfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gfb_validation.pdf.gz | 453 KB | Display | wwPDB validaton report |
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Full document | 4gfb_full_validation.pdf.gz | 463.7 KB | Display | |
Data in XML | 4gfb_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 4gfb_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gf/4gfb ftp://data.pdbj.org/pub/pdb/validation_reports/gf/4gfb | HTTPS FTP |
-Related structure data
Related structure data | 3ukgS S: Starting model for refinement |
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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
#1: Protein | Mass: 31988.744 Da / Num. of mol.: 1 / Fragment: 358-596 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: RAP1, GRF1, TUF1, YNL216W, N1310 / Production host: Escherichia coli (E. coli) / References: UniProt: P11938 |
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#2: DNA chain | Mass: 9398.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
#3: DNA chain | Mass: 9668.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
#4: Chemical | ChemComp-CA / |
#5: 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: 2.86 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: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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