+Open data
-Basic information
Entry | Database: PDB / ID: 8ya8 | ||||||
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Title | The crystal structure of human Rtel1 HHD2 domain | ||||||
Components | Regulator of telomere elongation helicase 1 | ||||||
Keywords | HYDROLASE / Regulator of telomere elongation helicase 1 / DNA BINDING PROTEIN | ||||||
Function / homology | Function and homology information DNA strand displacement / telomeric loop disassembly / negative regulation of telomere maintenance in response to DNA damage / positive regulation of telomeric loop disassembly / telomere maintenance in response to DNA damage / positive regulation of telomere maintenance via telomere lengthening / negative regulation of t-circle formation / Cytosolic iron-sulfur cluster assembly / mitotic telomere maintenance via semi-conservative replication / negative regulation of DNA recombination ...DNA strand displacement / telomeric loop disassembly / negative regulation of telomere maintenance in response to DNA damage / positive regulation of telomeric loop disassembly / telomere maintenance in response to DNA damage / positive regulation of telomere maintenance via telomere lengthening / negative regulation of t-circle formation / Cytosolic iron-sulfur cluster assembly / mitotic telomere maintenance via semi-conservative replication / negative regulation of DNA recombination / positive regulation of telomere maintenance / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / DNA duplex unwinding / regulation of double-strand break repair via homologous recombination / replication fork processing / positive regulation of telomere capping / Telomere Extension By Telomerase / DNA polymerase binding / DNA helicase activity / telomere maintenance / 4 iron, 4 sulfur cluster binding / nuclear membrane / DNA helicase / chromosome, telomeric region / nuclear speck / DNA repair / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Chun, I.S. / Kim, M.S. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To Be Published Title: The crystal structure of human Rtel1 HHD2 domain Authors: Chun, I.S. / Kim, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ya8.cif.gz | 115.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ya8.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 8ya8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ya8_validation.pdf.gz | 468.9 KB | Display | wwPDB validaton report |
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Full document | 8ya8_full_validation.pdf.gz | 472.4 KB | Display | |
Data in XML | 8ya8_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 8ya8_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/8ya8 ftp://data.pdbj.org/pub/pdb/validation_reports/ya/8ya8 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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2 |
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7 |
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Unit cell |
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-Components
#1: Protein | Mass: 9737.107 Da / Num. of mol.: 7 / Fragment: HHD2 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RTEL1, C20orf41, KIAA1088, NHL / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZ71, DNA helicase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 53.39 % |
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Crystal grow | Temperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M Potassium sulfate, 20% (v/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. obs: 14421 / % possible obs: 94.3 % / Redundancy: 3.8 % / CC1/2: 0.999 / Net I/σ(I): 8.09 |
Reflection shell | Resolution: 2.85→2.95 Å / Mean I/σ(I) obs: 1.59 / Num. unique obs: 1393 / CC1/2: 0.766 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→48.9 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→48.9 Å
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Refine LS restraints |
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LS refinement shell |
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