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- PDB-8sh1: Structure of human POT1 DNA binding domain bound to a 5'-phosphor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8sh1 | |||||||||||||||
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Title | Structure of human POT1 DNA binding domain bound to a 5'-phosphorylated junction of a telomeric double-stranded DNA duplex with a 3'-overhang | |||||||||||||||
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![]() | DNA BINDING PROTEIN/DNA / shelterin / telomere / DNA junction / 5'-phosphorylated / POT-hole / chromosome end protection / POT1 / DBD / POT1-DNA complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | |||||||||||||||
Function / homology | ![]() positive regulation of DNA strand elongation / regulation of DNA helicase activity / positive regulation of DNA helicase activity / G-rich single-stranded DNA binding / telomere assembly / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of double-strand break repair via nonhomologous end joining / positive regulation of helicase activity / telomerase inhibitor activity ...positive regulation of DNA strand elongation / regulation of DNA helicase activity / positive regulation of DNA helicase activity / G-rich single-stranded DNA binding / telomere assembly / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of double-strand break repair via nonhomologous end joining / positive regulation of helicase activity / telomerase inhibitor activity / DEAD/H-box RNA helicase binding / establishment of protein localization to telomere / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / regulation of telomere maintenance via telomerase / Telomere C-strand (Lagging Strand) Synthesis / : / positive regulation of telomere maintenance / nuclear telomere cap complex / single-stranded telomeric DNA 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 / DNA duplex unwinding / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / Telomere Extension By 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 / positive regulation of telomere maintenance via telomerase / Inhibition of DNA recombination at telomere / Meiotic synapsis / DNA Damage/Telomere Stress Induced Senescence / chromosome, telomeric region / nucleoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Nandakumar, J. / Tesmer, V.M. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Human POT1 protects the telomeric ds-ss DNA junction by capping the 5' end of the chromosome. Authors: Tesmer, V.M. / Brenner, K.A. / Nandakumar, J. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 205.4 KB | Display | ![]() |
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PDB format | ![]() | 136.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.5 KB | Display | ![]() |
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Full document | ![]() | 443.5 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sh0C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 33811.828 Da / Num. of mol.: 1 / Fragment: DNA binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Details (production host): human POT1 aa 1-299 cloned downstream of a sumo-star tag in the pFastBac vector with an N-terminal His tag Cell line (production host): High Five / Production host: ![]() |
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#2: DNA chain | Mass: 6879.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: DNA chain | Mass: 3029.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.96 Å3/Da / Density % sol: 75.21 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: hDBD complex with 5prime-P-ds-ss1-12 was crystallized at 16C by the sitting drop method in a drop containing 0.5 microliter 14 mg/ml protein-DNA complex (in 25 mM Tris (pH 8), 100 mM NaCl, ...Details: hDBD complex with 5prime-P-ds-ss1-12 was crystallized at 16C by the sitting drop method in a drop containing 0.5 microliter 14 mg/ml protein-DNA complex (in 25 mM Tris (pH 8), 100 mM NaCl, and 2 mM DTT) and 0.5 microliter well solution (0.02 M MgCl2, 0.9 M Hepes (pH 7.5), and 20% polyacrylic acid N100 sodium salt, derived from condition G2 of the JCSG+ screen (NeXtal). Crystals were harvested in 25 mM Tris (pH 8), 100 mM NaCl, 0.02 M MgCl2, 0.1 M Hepes (pH 7.5), and 22% polyacrylic acid N100 sodium salt and cryoprotected in harvesting solution supplemented with 35% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12713 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→86.98 Å / Num. obs: 27182 / % possible obs: 99.7 % / Redundancy: 13.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.146 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.6→2.72 Å / Num. unique obs: 45826 / CC1/2: 0.27 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 128.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→42.66 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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