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Yorodumi- PDB-7wu8: Crystal structure of Harmonin-homology domain 2 (HHD2) of human RTEL1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wu8 | ||||||
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Title | Crystal structure of Harmonin-homology domain 2 (HHD2) of human RTEL1 | ||||||
Components | Regulator of telomere elongation helicase 1 | ||||||
Keywords | PROTEIN BINDING / RTEL1 / Harmonin homology domain 2 / Protein-protein interaction / Protein-DNA interaction | ||||||
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 / 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 ...DNA strand displacement / telomeric loop disassembly / negative regulation of telomere maintenance in response to DNA damage / positive regulation of telomeric loop disassembly / 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 maintenance in response to DNA damage / Telomere Extension By Telomerase / DNA polymerase binding / telomere maintenance / DNA helicase activity / 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: 1.599 Å | ||||||
Authors | Kumar, N. / Rothweiler, U. / Singh, M. | ||||||
Funding support | India, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2024 Title: Harmonin homology domain-mediated interaction of RTEL1 helicase with RPA and DNA provides insights into its recruitment to DNA repair sites. Authors: Kumar, N. / Taneja, A. / Ghosh, M. / Rothweiler, U. / Sundaresan, N.R. / Singh, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wu8.cif.gz | 135.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wu8.ent.gz | 105 KB | Display | PDB format |
PDBx/mmJSON format | 7wu8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wu8_validation.pdf.gz | 468.2 KB | Display | wwPDB validaton report |
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Full document | 7wu8_full_validation.pdf.gz | 469.9 KB | Display | |
Data in XML | 7wu8_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 7wu8_validation.cif.gz | 43.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/7wu8 ftp://data.pdbj.org/pub/pdb/validation_reports/wu/7wu8 | 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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3 |
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4 |
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5 |
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6 |
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7 |
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Unit cell |
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-Components
#1: Protein | Mass: 10637.021 Da / Num. of mol.: 7 / Fragment: HHD2 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: 2.14 Å3/Da / Density % sol: 42.4 % / Description: Needle shaped crystal |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 20mM Tris pH7.4, 250mM NaCl, 5% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 11, 2020 / Details: Toroidal mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.599→48.336 Å / Num. obs: 80150 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.47 % / Biso Wilson estimate: 31.52 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.053 / Χ2: 0.98 / Net I/σ(I): 13.48 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AF-Q9NZ71-F1 Resolution: 1.599→48.156 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.177 / Average fsc free: 0.9054 / Average fsc work: 0.915 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.084 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.133 Å2
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Refinement step | Cycle: LAST / Resolution: 1.599→48.156 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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