+Open data
-Basic information
Entry | Database: PDB / ID: 1iv6 | ||||||
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Title | Solution Structure of the DNA Complex of Human TRF1 | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / TELOMERES / Protein-DNA complex / MYB DOMAIN / Helix-turn-helix / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / t-circle formation / telomeric D-loop disassembly ...positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / t-circle formation / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / Telomere C-strand (Lagging Strand) Synthesis / : / positive regulation of telomere maintenance / nuclear telomere cap complex / ankyrin repeat binding / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / telomere capping / Telomere Extension By Telomerase / DNA binding, bending / negative regulation of telomere maintenance via telomere lengthening / telomeric DNA binding / negative regulation of DNA replication / negative regulation of telomere maintenance via telomerase / telomere maintenance via telomerase / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Meiotic synapsis / Inhibition of DNA recombination at telomere / telomere maintenance / DNA Damage/Telomere Stress Induced Senescence / fibrillar center / spindle / chromosome, telomeric region / microtubule binding / nuclear body / cell division / nucleolus / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing | ||||||
Authors | Nishikawa, T. / Okamura, H. / Nagadoi, A. / Konig, P. / Rhodes, D. / Nishimura, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Structure / Year: 2001 Title: Solution structure of a telomeric DNA complex of human TRF1. Authors: Nishikawa, T. / Okamura, H. / Nagadoi, A. / Konig, P. / Rhodes, D. / Nishimura, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iv6.cif.gz | 734.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iv6.ent.gz | 612.2 KB | Display | PDB format |
PDBx/mmJSON format | 1iv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iv6_validation.pdf.gz | 379.7 KB | Display | wwPDB validaton report |
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Full document | 1iv6_full_validation.pdf.gz | 713.1 KB | Display | |
Data in XML | 1iv6_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 1iv6_validation.cif.gz | 46.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/1iv6 ftp://data.pdbj.org/pub/pdb/validation_reports/iv/1iv6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 4102.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Human natural telomeric sequence |
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#2: DNA chain | Mass: 3840.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Human natural telomeric sequence |
#3: Protein | Mass: 8598.949 Da / Num. of mol.: 1 / Fragment: DNA-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRF1 / Plasmid: pET13A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P54274 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 3D Sequential assignment protocol; 3D HNHA; 3D 15N separated NOESY, 3D 13C separated NOESY, 2D NOESY, 2D TOCSY and 2D COSY with or without isotope filtering |
NMR details | Text: The structures were determined by multi-dimensional heteronuclear -edited and -filtered NMR spectroscopy. |
-Sample preparation
Details | Contents: 1.5-2.5mM TRF1-DNA complex; 5mM Phosphate buffer with 10mM NaCl Solvent system: 90% H2O, 10% D2O or 100% D2O |
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Sample conditions | pH: 6.8 / Pressure: ambient / Temperature: 305 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: distance geometry, simulated annealing / Software ordinal: 1 Details: The structures were generated by 4-dimensional simulated annealing (4D-SA) with program EMBOSS, based on a total of 1341 experimental restraints, 901 and 356 are the NOE derived distance ...Details: The structures were generated by 4-dimensional simulated annealing (4D-SA) with program EMBOSS, based on a total of 1341 experimental restraints, 901 and 356 are the NOE derived distance restraints for protein and DNA, respectively, 29 are protein dihedral restraints and 55 are protein-DNA intermolecular restrainTs. In addition, 66 hydrogen bond and 221 ring-to-ring restraints are applied through 4D-SA to maintain the DNA base pair planarity. | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |