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Yorodumi- PDB-2e1f: Crystal structure of the HRDC Domain of Human Werner Syndrome Pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e1f | ||||||
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Title | Crystal structure of the HRDC Domain of Human Werner Syndrome Protein, WRN | ||||||
Components | Werner syndrome ATP-dependent helicase | ||||||
Keywords | HYDROLASE / HRDC domain | ||||||
Function / homology | Function and homology information 3'-flap-structured DNA binding / positive regulation of strand invasion / forked DNA-dependent helicase activity / telomeric G-quadruplex DNA binding / positive regulation of hydrolase activity / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of growth rate / telomere maintenance via semi-conservative replication / G-quadruplex DNA unwinding ...3'-flap-structured DNA binding / positive regulation of strand invasion / forked DNA-dependent helicase activity / telomeric G-quadruplex DNA binding / positive regulation of hydrolase activity / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of growth rate / telomere maintenance via semi-conservative replication / G-quadruplex DNA unwinding / t-circle formation / telomeric D-loop disassembly / Y-form DNA binding / four-way junction helicase activity / G-quadruplex DNA binding / MutLalpha complex binding / bubble DNA binding / Processive synthesis on the C-strand of the telomere / Impaired BRCA2 binding to PALB2 / Removal of the Flap Intermediate from the C-strand / protein localization to nucleolus / DNA 3'-5' helicase / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / response to UV-C / exonuclease activity / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA duplex unwinding / DNA metabolic process / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / 3'-5' DNA helicase activity / DNA synthesis involved in DNA repair / DNA unwinding involved in DNA replication / replication fork processing / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / SUMOylation of DNA damage response and repair proteins / four-way junction DNA binding / 3'-5' exonuclease activity / DNA helicase activity / telomere maintenance / cellular response to starvation / isomerase activity / replication fork / determination of adult lifespan / G2/M DNA damage checkpoint / double-strand break repair via homologous recombination / base-excision repair / HDR through Homologous Recombination (HRR) / cellular senescence / cellular response to gamma radiation / chromosome / double-strand break repair / Processing of DNA double-strand break ends / manganese ion binding / chromosome, telomeric region / DNA replication / Regulation of TP53 Activity through Phosphorylation / response to oxidative stress / Hydrolases; Acting on ester bonds / nuclear speck / chromatin binding / centrosome / DNA damage response / protein-containing complex binding / nucleolus / magnesium ion binding / protein homodimerization activity / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kitano, K. / Yoshihara, N. / Hakoshima, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Crystal structure of the HRDC domain of human Werner syndrome protein, WRN Authors: Kitano, K. / Yoshihara, N. / Hakoshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e1f.cif.gz | 30.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e1f.ent.gz | 20.1 KB | Display | PDB format |
PDBx/mmJSON format | 2e1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e1f_validation.pdf.gz | 404 KB | Display | wwPDB validaton report |
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Full document | 2e1f_full_validation.pdf.gz | 404.1 KB | Display | |
Data in XML | 2e1f_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | 2e1f_validation.cif.gz | 5.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/2e1f ftp://data.pdbj.org/pub/pdb/validation_reports/e1/2e1f | HTTPS FTP |
-Related structure data
Related structure data | 2e1eSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 11399.173 Da / Num. of mol.: 1 / Fragment: HRDC domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-5X-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus RIL References: UniProt: Q14191, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 / Details: pH 5.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: May 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 10934 / % possible obs: 99.7 % |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2E1E Resolution: 2→20 Å / Details: the structure was refined also with REFMAC 5.
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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