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Open data
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Basic information
Entry | Database: PDB / ID: 1ign | ||||||
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Title | DNA-BINDING DOMAIN OF RAP1 IN COMPLEX WITH TELOMERIC DNA SITE | ||||||
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![]() | DNA BINDING PROTEIN/DNA / RAP1 / YEAST / TELOMERES / HOMOEODOMAIN / DNA BINDING PROTEIN-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 / G-quadruplex DNA binding / double-stranded telomeric 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 / G-quadruplex DNA binding / double-stranded telomeric DNA binding / regulation of glycolytic process / silent mating-type cassette heterochromatin formation / 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 / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Koenig, P. / Giraldo, R. / Chapman, L. / Rhodes, D. | ||||||
![]() | ![]() Title: The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA. Authors: Konig, P. / Giraldo, R. / Chapman, L. / Rhodes, D. #1: ![]() Title: The Yeast Telomere-Binding Protein RAP1 Binds to and Promotes the Formation of DNA Quadruplexes in Telomeric DNA Authors: Giraldo, R. / Rhodes, D. #2: ![]() Title: Purification and Cloning of a DNA Binding Protein from Yeast that Binds to Both Silencer and Activator Elements Authors: Shore, D. / Nasmyth, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 142.3 KB | Display | ![]() |
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PDB format | ![]() | 103 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.57, 0.8216, -0.0054), Vector: Details | MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 360 .. A 594 B 360 .. B 594 0.62 | |
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Components
#1: DNA chain | Mass: 5673.695 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 5939.803 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | Mass: 28704.143 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: T7 PROMOTER / Gene: RAP1 DNA BINDING DOMAIN / Plasmid: PET3C / Gene (production host): RAP1 DNA BINDING DOMAIN 353 TO 598 / Production host: ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 49.1 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 49.1 % | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 22, 1995 |
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Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.25→16 Å / Num. obs: 33281 / % possible obs: 96 % / Observed criterion σ(I): 4 / Redundancy: 2.9 % / Rmerge(I) obs: 0.047 |
Reflection | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 16 Å / % possible obs: 96 % / Observed criterion σ(I): 4 / Redundancy: 2.9 % / Rmerge(I) obs: 0.047 |
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Processing
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Refinement | Resolution: 2.25→16 Å / σ(F): 2 Details: ESTIMATED COORD. ERROR 0.426 ANGSTROMS FINAL RMS COORD. SHIFT 0.111 ANGSTROMS
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Displacement parameters | Biso mean: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→16 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 16 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.219 / Rfactor Rfree: 0.294 / Rfactor Rwork: 0.219 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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